By Jacob Soboroff, Nicole Acevedo and Suzanne Gamboa

The Trump administration said it recently discovered 14 more migrant children who had been separated from their parents at the border and were not in the official count of separated minors.

The discovery raises the official number of children separated from families when the administration carried out its zero-tolerance policy to 2,668.

The U.S. Department of Health and Human Services (HHS) acknowledged the miscount Thursday night in federal court. In a court-ordered filing, the department's Office of Refugee Resettlement stated it learned this during a "review of case management records.”

As a result, the office has “recategorized” the detained children to reflect that they had been initially separated from their families.

For several months in the spring and summer and during a pilot project last year, the administration began prosecuting all people who crossed the border illegally. Children, including babies who came with adults, were taken into federal custody and separated from their parents. President Donald Trump, under pressure from the court and public, ended the separations.

The federal court also ordered the administration to reunite parents and children. The administration has been working with advocates to comply with the order for several months, including tracking down parents it deported without their children.

Mark Weber, HHS deputy assistant secretary, told NBC News that uncovering the 14 children is “more evidence that HHS continues to work to ensure compliance with [the] court order, and the safe and speedy reunification of separated children.”

But ACLU attorney Lee Gelernt fired back, saying advocacy organizations have been raising concerns that there might be more children who have been counted as "unaccompanied minors" — children who arrived at the border alone — instead of as separated from their families.

"As bad as it is that the administration has lost track of children, it hardly comes as a shock, given the lack of any plan to reunite the families,” Gelernt, deputy director of the ACLU's national Immigrants' Rights Project, told NBC News.

A GAO report released this week found that agencies had received no warning before the administration's implementation of its "zero tolerance" policy and were not prepared to handle the thousands of babies and children who were forcibly separated from their parents.

The report said that before April, when the zero-tolerance policy was implemented, the Department of Homeland Security and HHS did not have a consistent way to indicate in their data systems children and parents who had been separated at the border.

The systems were updated but "it is too soon to know the extent to which these changes, if fully implemented, will consistently indicate when children have been separated from their parents, or will help reunify families, if appropriate," the report said.

News of the "discovered" children comes as the administration has discussed imposing a new form of child separations and as Trump has stepped up his rhetoric on immigration, including threatening to send troops to the U.S.-Mexico border and to close it.

The threats are happening as many states are experiencing record-breaking early voting in this year's midterm elections that could determine control of Congress, as well as the governorships and partisan makeup of legislatures. There has also been a significant increase in the number of families arriving at the border.

Still in custody

Forty-seven children whose parents are “not eligible for reunification” or are “not available for discharge” are still in federal custody, according to court records. Thirty-three of the children’s parents already have been deported, raising worries among lawyers and advocates about the fate of their reunification.

Meanwhile, court documents show that the government has yet to provide detained families a timeline or plan for what happens next.

According to the filing, the government asked 258 mothers and children remain detained and have been given options on how to proceed, including being returned to their countries or "relief from removal."

At least 142 families reported they wished to seek “relief from removal.” However, because the administration has not come up with a timeline for the proceedings, there are concerns about the families being detained too long.

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