The Trump administration apologized in court for a “mistake” in the deportation of a Massachusetts college student who was detained trying to fly home to surprise her family in Texas for Thanksgiving.

But the administration still argued that the federal government error should not affect her immigration case.

Any Lucía López Belloza, a 19-year-old freshman at Babson College in Wellesley, 15 miles west of Boston, was detained at the city’s airport on 20 November and flown to Honduras two days later. Her sudden removal came despite an emergency court order on 21 November directing the government to keep her in Massachusetts or elsewhere in the United States for at least 72 hours for legal processes.

López Belloza, whose family emigrated from Honduras to the US in 2014 when she was seven, is currently staying with grandparents and studying remotely. She is not detained and was recently visiting an aunt in El Salvador. In early December, Immigration and Customs Enforcement (ICE) officers reportedly turned up at her parents’ home in Austin, Texas and behaved aggressively towards the family but left without taking further action.

At a federal court hearing on Tuesday of this week in Boston, the government argued the court lacks jurisdiction in the case because lawyers for López Belloza filed their action several hours after she was taken to Texas on the way out of the US in November. But the government also acknowledged it violated the judge’s order.

In court filings and in open court, government lawyers said an ICE deportation officer mistakenly believed the order no longer applied and he failed to activate a system that alerts other ICE officers that a case is subject to judicial review and that removal should be halted.

“On behalf of the government, we want to sincerely apologize,” said Mark Sauter, assistant US attorney, to the judge, saying the employee understands “he made a mistake”. The violation, Sauter added, was “an inadvertent mistake by one individual, not a willful act of violating a court order”.

In a declaration filed with the court on 2 January, the ICE officer also admitted he did not notify ICE’s enforcement office in Port Isabel, Texas, that the removal mission needed to be canceled. He said he believed the judge’s order did not apply once López Belloza was no longer in the state.

The government maintains, however, that her deportation was lawful because an immigration judge ordered the removal of López Belloza and her mother in 2016, and the Board of Immigration Appeals dismissed their appeal in 2017. Prosecutors said she could have pursued additional appeals or sought a stay of removal.

Her lawyer, Todd Pomerleau, countered that she was deported in clear violation of the 21 November order and said the government’s actions deprived her of due process. “I was hoping the government would show some leniency and bring her back,” he said. “They violated a court order.”

Federal Judge Richard Stearns said he appreciated the government acknowledging the error, calling it a “tragic” bureaucratic mistake. But he appeared to rule out holding the government in contempt, noting the violation did not appear intentional. He also questioned whether he has jurisdiction over the case.

“It might not be anybody’s fault, but she was the victim of it,” Stearns said, adding at one point that Lopez Belloza could explore applying for a student visa.

Pomerleau said one resolution would be allowing López Belloza to return to finish her studies while he works to reopen the underlying removal order.

The Associated Press contributed reporting.