ALEXANDRIA, Va. — A Justice Department lawyer on Thursday defended the legality of Lindsey Halligan's appointment as acting U.S. attorney to a skeptical federal judge who's weighing whether to dismiss cases she brought against former FBI Director James Comey and New York Attorney General Letitia James.

U.S. District Judge Cameron Currie did not issue a ruling after the hour-plus-long hearing, but said she plans to issue a decision by Thanksgiving on whether to disqualify Halligan from her post.

An attorney for the Justice Department, Henry Whitaker, characterized questions about the appointment of Halligan — a Trump ally with no prosecutorial experience — as a "paperwork error."

Currie made clear, however, that she had serious concerns, including over what appeared to be gaps in the transcript of the grand jury proceedings in the Comey case.

Attorneys for Comey and James made their arguments in a rare joint hearing before Currie, who traveled up from the District of South Carolina to avoid potential conflicts of interest that could come into play if local federal district judges, who could be involved in appointing a Halligan replacement, presided over the case.

Halligan presented the cases against Comey and James to grand juries on her own, and was the only person to sign off on their indictments. Lawyers for Comey and James contend that because her appointment was unlawful, she was essentially a private citizen at the time, and the indictments against them should be tossed.

“When the only person presenting to the grand jury lacks government authority, it’s a fundamental error,” Comey attorney Ephraim McDowell told the judge.

James' lawyer, Abbe Lowell, told the judge that she wouldn't let a private citizen like Elon Musk present the case, so she shouldn't allow Halligan to do so either.

Currie, meanwhile, pressed the government on the transcript of the grand jury deliberations in Comey's case, which she'd previously ordered to be turned over to her.

She said there was a significant period of time missing in the grand jury material she reviewed, between 4:28 p.m. and when Comey was indicted later that evening. The judge said it was possible there was no court reporter in the room at the time, meaning only Halligan and the grand jury would have been in the room.

Currie also questioned a subsequent filing from U.S. Attorney Pam Bondi saying she’d reviewed and signed off on the proceedings.

"It became obvious to me that the attorney general could not have reviewed" that material because of the missing minutes, Currie said.

“She said she reviewed the proceedings,” Whitaker said.

“She could not have,” Currie shot back. “She reviewed the witness testimony,” Whitaker then replied, walking back his previous response.

In a court order earlier this month, Currie said the government had turned over witness testimony from the proceeding, but had not turned over "remarks made by the indictment signer" — Halligan — "both before and after the testimony of the sole witness," and directed the DOJ to do so.

The DOJ said in a court filing the next day that it had complied with her order.

The judge also pressed Whitaker on Bondi's having since named Halligan a "special attorney," and asked if he disagreed with the order that dismissed the case of U.S. versus Donald Trump in Florida — the criminal classified documents case against the then-former president.

U.S. District Judge Aileen Cannon tossed the case last year on the grounds that then-Attorney General Merrick Garland didn't have the power to appoint a special counsel.

Whitaker said he disagreed with the notion that the A.G. can't make appointments.

Currie, a Bill Clinton appointee, heard the arguments instead of a judge from the Eastern District of Virginia to avoid any potential intradistrict conflict of interest.

Halligan, who was part of Trump’s legal team in the Mar-a-Lago classified documents case, was sworn in as interim U.S. attorney in one of the nation’s busiest federal court districts on Sept. 22. That’s three days after Erik Siebert, the U.S. attorney who had been serving in the role since Jan. 21, resigned after being pressured to indict Comey and James.

The indictments against Comey and James came after Trump publicly urged Attorney General Pam Bondi to take action against Comey, James and another of the president’s adversaries, Sen. Adam Schiff, D-Calif. Comey and James both pleaded not guilty to their respective charges.

Critics say that the indictments are part of a troubling pattern of Trump going after his perceived political foes. John Bolton, who served as national security adviser during Trump's first term but has since become a staunch opponent of the president, was also indicted in October.

According to federal statute, individuals may only serve for 120 days after being appointed U.S. attorney, unless confirmed by the U.S. Senate before then. The Senate had not confirmed him, but district judges of the Eastern District of Virginia exercised their own independent appointment authority to legally retain Siebert as an interim U.S. attorney beyond the 120-day limit.

It is that 120-day limit that James and Comey’s attorneys argue should not start back at zero with the appointment of Halligan.

Lowell told the judge the 120 days is designed to give a new president leeway “for a limited period of time to get the office moving.”

Comey was charged in late September with making a false statement to Congress during a September 2020 Senate Judiciary Committee hearing. Asked by Sen. Ted Cruz, R-Texas, about testimony he gave in 2017 asserting that he did not authorize the leak of information to the media about an FBI investigation into the "Clinton administration," Comey said, “I stand by the testimony.”

Trump first clashed with Comey during his first term over the then-FBI director's handling of the federal investigation Trump campaign's alleged ties to Russia. Comey was fired in May 2017 and has been an outspoken critic of Trump since then.

The Justice Department laid out in court papers that it believes the indictment of Comey — signed only by Halligan and unsealed days before the five-year statute of limitations expired — should survive this challenge to Halligan’s appointment regardless of what Currie decides because of U.S. Code 3288, the statute that governs this very issue.

“Whenever an indictment or information charging a felony is dismissed for any reason after the period prescribed by the applicable statute of limitations has expired, a new indictment may be returned in the appropriate jurisdiction within six calendar months of the date of the dismissal of the indictment or information,” the statute reads in part.

This six-month grace period, legal experts tell NBC News, may be the DOJ’s key to a continued prosecution of the former FBI director. Comey is asking the judge to dismiss his case "with prejudice," meaning it can't be refiled.

The bank fraud charge that James, who sued Trump and his businesses for fraud in 2022, is facing is well within the 10-year statute of limitations, and Lowell acknowledged to Currie his client could be indicted again by someone "with the right authority."

Both Comey and James are also seeking to have their cases dismissed before different judges on the grounds that they’re victims of “selective and vindictive” prosecutions.

Bondi has taken steps in recent weeks to shore up Halligan’s position.

On Oct. 31, Bondi issued a formal order retroactively appointing Halligan to the position of “special attorney” within the Department of Justice as of Sept. 22 — three days before Comey was indicted — and wrote, “Should a court conclude that Ms. Halligan’s authority as Special Attorney is limited to particular matters, I hereby delegate to Ms. Halligan authority as Special Attorney to conduct and supervise the prosecutions” of Comey and James.

McDowell told the judge that the strategy “cannot possibly work,” and that the government hadn’t cited any authority someone can retroactively be assigned a “special attorney.”

Halligan is facing several Bar Association complaints in Florida and Virginia, filed by the left-leaning watchdog group Campaign for Accountability.

“Ms. Halligan’s actions appear to constitute an abuse of power and serve to undermine the integrity of the Department of Justice (DOJ) and erode public confidence in the legal profession and the fair administration of justice,” the complaint says.