The Department of Justice (DoJ) told a federal judge Tuesday that it may have mistakenly separated a father and toddler who could both be US citizens for as long as a year, in the process of enforcing the Trump administration’s “zero-tolerance” immigration policy.

The American Civil Liberties Union (ACLU) called the revelation “horrific” and blamed the administration’s poor execution of the practice of family separations.

“The fact that a citizen got caught up in this mess shows just how poor the government’s record-keeping was, and this is just the latest example,” said Lee Gelernt, the deputy director of the ACLU’s Immigrants’ Rights Project.

On 26 June, in a suit filed by the ACLU against the government over the separation of families at the southern border, federal judge Dana Sabraw granted a preliminary injunction requiring the reunification of children under the age of five by 10 July.

In a hearing on Tuesday, just before the deadline, the DoJ was asked to account for each failed reunification of the 102 younger children in its care. It noted 27 cases where it found reunification was not currently feasible, including one “because the parent’s location has been unknown for more than a year … and records show the parent and child might be US citizens”.

Previously the DoJ had only revealed that the child’s father could not be located. The ACLU and the court were only made aware that both father and child might be US citizens on Tuesday.

“It actually happens much more frequently than you would believe,” Gelernt said. “They [Immigration and Customs Enforcement] make mistakes.”

In total the DoJ said it expected to have 38 children under five reunified by Tuesday’s 10pm PT deadline, 16 “soon thereafter” and another 20 depending on a number of conditions including whether or not parents can be located, and “if those parents request reunification”.

In Tuesday’s hearing, Sabraw said that the families were improperly separated and that he would not extend the deadline, meaning that the government is technically in violation of the court order as of Tuesday night. “These are firm deadlines. They’re not aspirational goals,” Sabraw said.

The complications the government has run into complying with Sabraw’s order foretell a troubled road ahead. Children under five represent just 5% of the 2,000 to 3,000 – the government has admitted it does not have an exact figure – who have been separated from their parents in recent months. Sabraw’s injunction requires the remaining 1,900 be reunified by 26 July.

The identity of the children and parents as provided to the judge by the government under court order are currently shielded by law.

The Legal Aid Society in New York said it is representing at least two of the separated children under five.

One boy, from El Salvador, was due to be released to his mother, according to Beth Krause, the supervising attorney of Legal Aid’s Immigrant Youth Project.

“I have no details about where, when, under what conditions,” she wrote in an email on Tuesday morning. The other boy, from Honduras, would remain with a foster family while the father remained in government custody, although it was not clear to her why.

“I know very, very little about this case,” she said. “It’s all very frustrating.”

The revelation comes on the same day that the Trump administration announced it would be implementing an ankle monitor system to track migrant families – a decision that was forced by Sabraw’s injunction and another federal court decision that came down on Monday.

After Trump signed an executive order ending his administration’s family separation policy in June, agencies had planned to detain families and children together until the parents’ immigration proceedings were complete, a process that can take months. That proposal ran afoul of the decades-old Flores v Reno settlement, which stipulates that migrant children cannot be held in detention for more than 20 days.

On Monday, another federal judge in California rejected a DoJ request to allow the long-term detention of migrant children, meaning that they could no longer separate families or hold them together in detention without running afoul of the federal courts.

Reuters contributed to this story