The Trump administration has quietly resumed separating immigrant families at the border, in some cases using vague or unsubstantiated allegations of wrongdoing or minor violations against the parents, including charges of illegally re-entering the country, as justification.

Over the last three months, lawyers at Catholic Charities, which provides legal services to immigrant children in government custody in New York, have discovered at least 16 new separation cases. They say they have come across such instances by chance and via their own sleuthing after children were put into temporary foster care and shelters with little or no indication that they arrived at the border with their parents.

ProPublica stumbled upon one more case late last month after receiving a call from a distraught Salvadoran father who had been detained in South Texas, and whose 4-year-old son, Brayan, had literally been yanked from his grasp by a Customs and Border Protection agent after they crossed the border and asked for asylum. Julio, the father, asked to be identified only by his first name because he was fleeing gang violence and worried about the safety of relatives back home.

“I failed him,” said Julio, 27, sobbing uncontrollably. “Everything I had done to be a good father was destroyed in an instant.”

ProPublica tracked down Brayan, who has reddish-blond hair and an endearing lisp, at a temporary foster care agency in New York City, and reached out to the lawyer who represents him. Until that phone call, the lawyer, Jodi Ziesemer, a supervising attorney at Catholic Charities, had no idea that Brayan had been separated from his father. The chaos, she said, felt disturbingly like zero tolerance all over again.

“It’s so disheartening,” Ziesemer said “This was supposed to be a policy that ended.”

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Officially it has. On June 20, President Donald Trump signed an executive order retreating from his so-called zero-tolerance immigration enforcement policy, which called on authorities to criminally prosecute adults caught illegally crossing the border and separate them from any children they brought with them. A week later, a federal judge, Dana M. Sabraw, issued an injunction against the separations and ordered the government to put the thousands of affected families back together.

Sabraw, however, exempted cases in which the safety of the child was at risk, and crucially, imposed no standards or oversight over those decisions. As a result, attorneys say, immigration officials — taking their cues from an administration that has made it clear it still believes family separations are an effective deterrent — are using whatever justification they can find, with or without substantiation, to deem immigrant parents unfit or unsafe.

“If the authorities have even the most specious evidence that a parent was a gang member, or had some kind of blemish on their record,” said Neha Desai, a senior attorney at the National Center for Youth Law, “anything they can come up with to say that the separation is for the health and welfare of the child, then they’ll separate them.”

In an email, a senior CBP official acknowledged that immigrant families are still being separated, but said the separations had “nothing to do with zero tolerance.” The official added that “this administration continues to comply with the law and separates adults and children when required for the safety and security of the child.” The official declined to say how many children have been taken from their parents for what was said to be their own protection.

CBP officials explained that Brayan was such a case. One official said that the agency had conducted a routine background check on Julio, and that it “confirmed his gang affiliation with MS-13.” Spokeswoman Corry Schiermeyer declined to provide the evidence the agency had to support the allegation, saying only that it was “law enforcement sensitive.” Nor would she say why CBP believed Julio was a danger to his child. But Sabraw’s order, she said, “did not prevent these separations, in fact it explicitly allows DHS to continue with this prior practice.”

CBP has also not shared any evidence supporting its assertion of Julio’s gang ties with his lawyer, Georgia Evangelista, who said she wonders whether it exists.

(On Tuesday, a government lawyer repeated the allegation to an immigration judge in South Texas but said he could not provide documentation to the court because it was “confidential,” according to Evangelista. She said the immigration judge did not press for release of the evidence but freed her client on an $8,000 bond. Evangelista was frustrated by the outcome, saying, “How can we fight these charges when we don’t know what they are.”)

According to Evangelista, Julio arrived at the border in mid-September, carrying a letter prepared by a Salvadoran lawyer that explained that he had fled El Salvador with his son because he had been attacked and threatened by gangs there for years. At Evangelista’s request, the Salvadoran lawyer and Julio’s former employer sent sworn statements vouching for Julio’s character, and stating that he was never involved in criminal activity.

“I’m furious about this. They aren’t playing by the rules,” Evangelista said, referring to U.S. immigration authorities. “They’re treating him like a criminal so they can justify taking away his son. Where’s the proof? It’s his word against theirs. It sickens me.”

Susan Watson, a civil rights and family lawyer, said this kind of action could not be done without a judge’s review in custody cases that do not involve immigration issues. “Constitutionally, before a parent is separated from a child, you are entitled to due process,” she said. “Some decision in a dark corner by the Border Patrol doesn’t meet that standard.”

In New York, Ziesemer says the new separations identified by her organization involve children between the ages of 2 and 17, including Brayan. All of them arrived in New York City without any records indicating they had been separated from their parents at the border and why. A few weeks ago, the ACLU, which brought the lawsuit over the first round of family separations, sent a letter to the Justice Department raising concerns about the new cases, specifically about the grounds for the separations and why the ACLU hadn’t been notified about them.

Lee Gelernt, the ACLU attorney who led the organization’s lawsuit against family separations in the spring, said, “If the government is still secretly separating children, and is doing so based on flimsy excuses, that would be patently unconstitutional and we will be back in court.”

Lawyers at the ACLU and Catholic Charities said that the DOJ responded that it wasn’t obligated to report the new separations to the ACLU because they hadn’t been done as a part of the zero-tolerance policy. The DOJ said that in 14 of the 17 cases flagged in the ACLU’s letter, the children were removed from their parents’ custody because authorities suspected the parents had some kind of criminal background that made them unfit — even dangerous. But the agency would not specify what crimes the parents were suspected of committing and what evidence authorities had to support these allegations.

The ACLU and other groups representing immigrant children said the DOJ’s secrecy is highly troubling on several counts. They worry that the Department of Homeland Security has allowed authorities without formal training in custody issues — primarily Border Patrol agents — to make decisions using standards that could violate the spirit of the court order and that would never hold up in non-immigration cases. Ziesemer has talked to relatives and social workers and says she suspects that at least eight of the cases involve parents whose crime is illegally re-entering the country. Illegal re-entry is a felony, although previous administrations did not typically separate families in such cases. Ziesemer said the allegations the government has advanced to justify separations in eight other cases were either vague or unsubstantiated. The final case she identified involved a parent who was hospitalized.

“The government’s position is that because these are not zero-tolerance cases, they don’t have to tell us, or anyone, about them,” Ziesemer said. “Our position is that when children are separated from their parents, there needs to be some oversight.”

Brayan’s case is a vivid example of how government officials are interpreting the court order to allow separations of families.

I found out about him by accident. Early last month, after the government reported that of the more than 2,600 immigrant children separated under the zero-tolerance policy, only one child under the age of 5 remained in their care. I decided to try to find that child, thinking the case might make a compelling bookend to a story I’d written this year about a girl named Alison Jimena Valencia Madrid, whose cries were recorded inside a Border Patrol detention facility in June. The recording ignited a storm of outrage that tipped the political scales against the Trump administration’s family separation policy.

An attorney on the border, Thelma O. Garcia, said she represented a 6-year-old Salvadoran boy named Wilder Hilario Maldonado Cabrera, who was in a temporary foster home in San Antonio. Wilder had been separated from his father in June, Garcia said, and hadn’t been reunited because the father had a 10-year-old warrant for a DUI charge in Florida.

The father, Hilario Maldonado, called me from the South Texas detention facility in Pearsall and said he’d tried to keep in touch with Wilder by phone, but his social worker didn’t always pick up. When they did connect, he said, Wilder, pudgy, precocious and missing his two front teeth, scolded him for not coming to take him home.

I told Maldonado that it appeared he would be one of the last parents to go through such a separation because the government had agreed to stop them.

Maldonado, 39, said that wasn’t true. The separations are still happening, he said, and he knew of one.

A few minutes later, I got a call from Julio, who was at the same detention facility. He sounded desperate, crying and pleading for answers. He said he’d turned himself and Brayan into the authorities as soon as they’d crossed the border, asked for asylum and told immigration agents that his mother, who lives in Austin, Texas, was willing to help him get on his feet. Seven days later, a Border Patrol agent took Brayan, dressed in a SpongeBob SquarePants T-shirt, away, screaming.

Julio said all he knew was that his son was somewhere in New York. As soon as we hung up, I called Ziesemer at Catholic Charities, which has a government contract to provide legal services to the unaccompanied minors in the city. I asked whether she’d heard of Brayan.

“We do know this kid,” Ziesemer quickly responded, “but were not aware he was separated from his father.”

Ziesemer was audibly shaken. “Until you called, all I had was his name on a spreadsheet,” she said.

Ziesemer immediately arranged to have Brayan, who had been placed in a temporary foster home, brought to her office. Her experience told her not to expect much from their first interaction, partly because Brayan was likely to be afraid, and partly because he was only 4. So she tried putting Brayan at ease by opening a box of crayons and a Spider-Man coloring book.

He warmed up to her quickly, putting down his crayons to show her his Spider-Man moves and squiggling lines on a piece of paper when she asked whether he knew how to write his name. But, as Ziesemer expected, he was too young to make sense of what had happened to him on the border, much less explain it to an adult he’d just met. And his lisp made it hard for Ziesemer to understand the few things he could tell her.

After the meeting, she sounded both exasperated about having to grill a tiny child and terrified that there might be other children like him buried in her spreadsheets.

“We, and the caseworkers and the consulates, do what we can to fill in the gaps and figure out where these kids came from,” she said. “But that means days and weeks go by with a child not knowing where his parents are and vice versa. And it doesn’t have to be that way. It shouldn’t be that way.”

After Ziesemer’s meeting with Brayan, I traveled to Pearsall to meet Julio. He said he’d fled the country with Brayan because street gangs had threatened to kill him after finding out that he reported one of their members to the police. His wife and stepson stayed behind because there wasn’t enough money to pay for everyone to come. I spoke to his wife, who told me she was hiding out at her parents’ house because she didn’t want to be home if gang members came looking for her husband.

In photos his relatives sent, Julio looked sort of like a cop, stocky with a crew cut. But after a month in detention, he looked pale and deflated. He wore navy blue detention garb and his dark brown hair was wet, though neatly combed. He didn’t have any tattoos, which are common among Central American gang members.

Through tears, Julio told me he’d replayed the days since his arrival at the border in his mind, trying to make sense of why authorities took away his son. Julio and Brayan had been taken to the “ice box,” a notorious air-conditioned cellblock that is the first stop for most immigrants intercepted at the border. Brayan developed a high fever and had to be taken to the hospital for treatment. A Border Patrol agent who drove Julio and his son scolded Julio for bringing a small boy on such a harrowing trip. Could that be the reason they took his son away? Was it because the agents had looked at the color of Brayan’s hair and didn’t believe he was the boy’s father?

Julio wonders whether he had been fooled into signing a document at the hospital — they were all in English — surrendering his rights to his child. Was it because he’d once been arrested for a robbery in El Salvador, but exonerated two days later when authorities realized they had the wrong person? Why would they consider him a danger to his child?

It wasn’t until I told him that Julio learned his child had been taken from him because Border Patrol agents suspected he was a gang member. The news hit him hard, and it was confounding because at the same time the CBP had deemed him a gang member, another agency within DHS had found that his asylum petition, in which Julio claims he was a victim of gang violence, was persuasive enough to be heard by an immigration judge.

In early October, Julio had met with an asylum officer for what’s known as a credible fear interview. According to the report of that interview, which Julio provided to ProPublica, the asylum officer not only asked him why he fled El Salvador, but whether he had a criminal record. Among the questions were: Have you ever committed a crime in any country? Have you ever harmed someone for any reason? Even if you did not want to, have you ever helped someone else harm people? Have you ever been arrested or convicted of a crime? Have you ever been a member of a gang?

Julio answered no to all of them. The asylum officer who conducted the interview deemed Julio’s account credible, and, even more significantly, indicated that she had been provided no derogatory information or criminal records that would automatically bar Julio from winning asylum.

The discrepancy reflects differences in the legal standards for asylum and family separation. While the asylum officer’s decision is subject to review by a judge, the Border Patrol’s decision to take away Julio’s child was not.

“I don’t know what information, if any, they really have on Julio,” his attorney, Evangelista, said. “They have total discretion when it comes to separating him from his child. They can do what they want. And they don’t have to explain why.”

Julio said his own father had abandoned him when he was about Brayan’s age. Then his mother left for the United States when he was 7. He said he vowed never to do the same thing to Brayan, which is why he didn’t leave the boy behind in El Salvador. He wonders now whether that was a mistake. In every phone call with Brayan, Julio says, he feels his son slowly slipping away.

“He tells me: ‘You’re not my Papa anymore. I have a new Papa,’” Julio said of his son, adding: “He doesn’t even call me Papa. He calls me Papi. I never taught him that word.”

Back in New York, Ziesemer said she worries family separations may be beginning all over again.

Sitting with Brayan in her office, she said, brought back the faces of the 400 or so separated kids who had shuffled through over the summer. As Catholic Charities’ point person during the crisis, she said she came to know every single one of those kids by name. One 9-year-old girl went into a full panic attack when she was asked to step into a room without her sister because she thought Ziesemer was going to take her sister away like officials had taken her mother. “At one point, we had to have a meeting with the entire office to explain why the conference room was full of all these wailing kids,” she said.

Catholic Charities, the ACLU and several other large immigrant advocacy groups took the lead in putting the families together again; working the phones to find parents who were still in immigration detention and dispatching colleagues to Central America to track down parents who had already been deported. In addition to the “huge, heavy lift” of reunification, Ziesemer said, there was a crush of calls and emails from Congress, consulates and the media — all seeking information about the separations.

Ziesemer said she and her team worked around the clock for months, and though there are still several dozen kids awaiting reunification, she thought things were winding down. That’s when she began seeing new cases, like Brayan’s, which had some of the same hallmarks of the old ones.

Ziesemer didn’t know much about Brayan, except the little bit of information she’d gotten from him during their meeting. So I shared with her some of the things I’d learned about him from his family: that he could eat four hard-boiled eggs in one sitting; that he loved Lightning McQueen, a character from the Pixar movie “Cars”; and that he had a dog, Lucky, whom he insisted on seeing during every WhatsApp video call with his mother. His grandmother in Austin had fixed up a bedroom for him, filled with Mickey Mouse dolls, remote-control cars and winter coats. I told Ziesemer how distraught Brayan’s father was that his son called him “Papi.”

“A couple of weeks is a long time for a kid his age,” she said about Brayan. “They start losing attachments to people, even their parents.”