An official from the Department of Homeland Security said in an emailed statement that the agency is "complying with the court's order, and upon arrival in El Salvador, the plaintiffs did not disembark and are now en route back to the United States".
"This is pretty outrageous", said U.S. District Court Judge Emmet G. Sullivan after being told about the removal.
In a federal courtroom in Washington on Thursday, a federal judge heard about something the Trump administration had just done that clearly angered him.
"I'm not happy about this at all", Sullivan said.
The ACLU said later that government attorneys confirmed to them after the hearing that the pair was on a flight en route to El Salvador. The Justice Department declined to comment on the judge's threat of contempt. 'Someone seeking justice in USA court is spirited away while her attorneys are arguing for justice for her?' the judge asked.
"We are complying with the court's requests, and upon arrival in El Salvador, the plaintiffs will not disembark and will be promptly returned to the United States", a Department of Homeland Security official told CNN.
The government said it is racing to comply with the court's order.
But while in court arguing that deportation of their plaintiffs should be delayed, ACLU attorneys learned on Thursday that Carmen and her daughter were already in the process of being deported.
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In addition to ordering the government to get the mother and daughter back, Sullivan blocked the Trump administration from deporting eight other immigrants - now held in detention - who are part of the same lawsuit against the government for allegedly wrongfully rejecting their claims for asylum.
But their case was halted when officers found they did not have a "credible fear of persecution".
Successful applicants typically enter the country to flee persecution due to their race, religion, nationality or political views.
What about the ACLU lawsuit?
Asylum seekers previously had to show that the government in their native country was "unable or unwilling" to protect them. Many disappear instead of showing up. The memo argues that only traditional interpretations of asylum eligibility, such as those persecuted by governments for their religion or politics, are valid and that recent innovations like granting asylum to people who face ordinary crime in their home countries will no longer be tolerated.
ACLU attorney Jennifer Chang Newell declared this week in a statement that changing the standard was 'a naked attempt by the Trump administration to eviscerate our country's asylum protections'. In the suit, Grace said her partner of 22 years, and his two gang member sons from another relationship, repeatedly beat and threatened to kill her and her children. That number is more than triple what it was when Barack Obama became president in 2009.
There are about 700,000 backlogged asylum cases crawling through federal courts, according to the DOJ.