Federal judges in Alexandria, Virginia, have lashed out at the Justice Department as they continue to list Lindsey Halligan on court documents — some going as far as striking her name from paperwork from the bench.

Two magistrate judges and a district court judge in Alexandria, Virginia, told prosecutors in open court they didn’t believe Halligan’s name should be on new criminal case filings, such as guilty plea documents and indictments, after a decision in the district last week said she is not the US Attorney.

One of those judges, Magistrate William Fitzpatrick, said at a criminal case hearing Tuesday that filing criminal charging papers “under Ms. Halligan’s name” at this time “is simply not acceptable,” according to a transcript obtained by CNN.

Both Fitzpatrick and another judge in the district, Michael Nachmanoff, told prosecutors this week they believed the ruling was clear that Halligan wasn’t the US attorney for all cases. They both noted, in separate hearings this week, according to court transcripts, that the Justice Department hadn’t appealed the ruling about Halligan, nor asked any court to pause it for a possible appeal.

“The law in this district right now is that she is not and has not been the United States Attorney,” Fitzpatrick said on Tuesday.

The bombshell ruling last week, from Judge Cameron McGowan Currie, determined Halligan was not the US attorney because she hadn’t been Senate confirmed after 120 days of a vacancy in the post nor sworn in by the judges of the court. McGowan’s decision also dismissed the criminal cases against former FBI Director James Comey and New York Attorney General Letitia James, finding Halligan’s work on them “void.”

Comey had pleaded not guilty to lying to Congress. James had pleaded not guilty to mortgage fraud.

Nachmanoff, who oversaw the Comey case at the trial level, decided in a separate hearing Thursday for a Honduran man illegally in the US that Halligan’s name would need to be struck from that man’s case records.

He said he was finding it “difficult to reconcile” the court opinion with what the Justice Department is doing now, according to a transcript of the hearing Thursday.

CNN reached out to the Justice Department for comment.

During other criminal hearings on Tuesday, Fitzpatrick told a prosecutor that he would be striking Halligan’s name from criminal court documents, while another judge, Magistrate Lindsey Vaala, said she would annotate new indictments to acknowledge the ruling on Halligan.

The exchanges, captured on official audio recordings of the hearings and obtained first by CNN, emphasize a continued lack of formal explanation from Justice Department headquarters about why it believes Halligan can remain in the job.

“I agree with you that it is peculiar and we are in unusual territory,” Vaala told a different prosecutor later that afternoon, as she received newly approved indictments from prosecutors and the grand jury. She said “the concern” is accepting an indictment that has a signature block inconsistent with the previous judge’s decision.

She said she would put an asterisk on the documents and “a citation to Judge Currie’s decisions.”

“That’s perfectly fine with us, your honor,” the prosecutor, Tony Roberts, replied.

A footnote is now included next to Halligan’s name on at least two new criminal indictments this week, which identify the ruling on Halligan in the Comey and James cases, according to court records.

Falling actions in Comey and James cases

Attorney General Letitia James and former FBI Director James Comey.

The disarray over the Justice Department signatures on criminal court filings is part of the falling action of the dismissal of the criminal cases against Comey and James. Halligan secured the indictments alone in an afternoon session with a grand jury for each, just a few days after President Donald Trump called for the prosecution of the political foes and Attorney General Pam Bondi placed Halligan at the US Attorney’s Office.

Since the dismissals, Justice Department leadership has publicly continued to back her.

Halligan’s US Attorney’s Office is expected to attempt imminently to seek a renewed grand jury indictment of Comey, for alleged false statements to Congress. A grand jury in the district declined to charge James a second time on Thursday, but the Justice Department may try again, CNN reported this week.

Halligan is not expected to spearhead those grand jury presentations as she did the first time around for each, leaving other lower-level prosecutors to handle the cases in court.

The US Attorney’s Office has also tried to advise its dozens of prosecutors in at least five different internal guidance emails since last week how to sign their court filings, following the ruling on Halligan. At first, the prosecutors were told to remove her name and only list the top career prosecutor in the office, who serves as the first assistant US Attorney.

Since then, the prosecutors have been instructed to list Halligan’s name first at the bottom of criminal case filings, and also to list Deputy Attorney General Todd Blanche and the first assistant in the signature block.

The Justice Department’s reasoning for keeping Halligan’s name on criminal filings has been thin, from the perspective of prosecutors appearing in court.

Long-time prosecutor Tony Roberts told one judge that guidance his US Attorney’s Office received from the Justice Department’s Office of Legal Counsel, which sets policy and outlines legal reasoning for the executive branch, said to keep Halligan’s “name as is.”

“The Office of Legal Counsel told us to put the name as is as it has been presented on these indictments. That’s what we are going on at this point,” Roberts said in court on Tuesday, according to court records obtained by CNN.

The front of the Albert V. Bryan United States Courthouse in Alexandria, Virginia, on November 13.

“I believe there’s still internal deliberation what next steps the office needs to take. I understand that it’s peculiar,” the prosecutor added. “It’s something I’ve never seen in my 35 years, but we are following the Office of Legal Counsel’s guidance on this, and it’s not just purely an in-office decision.”

A Justice official familiar with the situation previously told CNN the DOJ prepared guidance after Currie’s ruling, to be sent to everyone in the Alexandria office, that said Halligan was still the US Attorney post.

But prosecutors in the office have felt left in the dark, and alarmed by the judges’ escalation of questions this week, sources familiar with the office now tell CNN.

“You’re in a terrible situation,” Fitzpatrick told one of the Eastern District of Virginia prosecutors on Thursday, according to the court transcripts. “And the fact that you have no guidance is tremendously disappointing, and that you have to stand here and take the brunt of this is patently unfair.”

CNN’s Evan Perez contributed to this report.