ALEXANDRIA, Va. (AP) — The prosecution of former FBI Director James Comey hit another hurdle Wednesday as the Justice Department acknowledged a possible lapse in how the case was presented to a federal grand jury for indictment.

The concession risked further imperiling a politically charged prosecution already subject to multiple challenges and demands for its dismissal. It came during a hearing in which Comey's lawyers asked U.S. District Judge Michael Nachmanoff to throw out the case on grounds that the government was being vindictive and as a separate challenge to Lindsey Halligan, the hastily appointed and inexperienced prosecutor who secured the indictment, is pending.

The revelation that the full grand jury did not review a copy of the final indictment is the latest indication of the Justice Department's seemingly disjointed pursuit of a criminal case against one of President Donald Trump's political enemies. Comey was fired by Trump in May 2017 while overseeing an FBI investigation into potential ties between Russia and Trump’s 2016 campaign. The two have been publicly at odds ever since, with Trump deriding Comey as “a weak and untruthful slime ball” and calling for his prosecution.

Concerns about the legal process came into focus earlier in the week when a different judge in the case raised questions about what he said were “profound investigative missteps,” including misstatements of the law to the grand jury and a potential breach of attorney-client privilege in the handling of evidence.

Halligan initially asked the grand jury to return a three-count indictment against Comey. But after the grand jurors rejected one of the proposed counts, the Justice Department that secured a second two-count indictment that accused Comey of making a false statement and obstructing Congress. Comey has pleaded not guilty and denied any wrongdoing.

In a blistering ruling Monday, U.S. Magistrate Judge William Fitzpatrick, also handling parts of the case, said he had reviewed a transcript of the grand jury proceedings and had questions about whether the full grand jury had reviewed the final two-count indictment that was returned.

The issue arose again on Wednesday when Nachmanoff, the trial judge, pressed the Justice Department about Fitzpatrick's concerns. After conferring privately with Halligan, Tyler Lemons, one of the prosecutors acknowledged that the revised indictment was not shown to all of the grand jurors.

“I was not there, but that is my understanding, your honor,” Lemons told the judge.

Nachmanoff called Halligan to the lectern and asked her who was in the courtroom when the final indictment was presented to a magistrate. She said only two grand jurors, including the foreperson, were there.

Comey lawyer Michael Dreeben called the government’s failure to present the final indictment to the entire grand jury grounds for dismissing the case. He also argued that the statute of limitations for the charged crimes has elapsed without a valid indictment.

“That would be tantamount to a bar of further prosecution in this case,” Dreeben said.

Nachmanoff did not issue an immediate decision, saying “the issues are too weighty and too complex” for a bench ruling.

Dreeben separately argued that the prosecution was improperly vindictive and rooted in Trump’s quest for retribution, circumstances requiring a dismissal.

“The president’s use of the Department of Justice to bring a criminal prosecution against a vocal and prominent critic in order to punish and deter those who would speak out against him violates the Constitution,” Dreeben said,

Though vindictive prosecution motions are not often successful, Comey’s lawyers have laid out a laundry list of verbal attacks from Trump in hopes of establishing the case as outgrowth of the president's hunger for retribution against the man who once served as his FBI director.

Trump amplified his long-running demands for a Comey prosecution with a September social media post in which he complained to Attorney General Pam Bondi about the lack of action against his political opponents. “We can’t delay any longer, it’s killing our reputation,” Trump wrote, adding that “JUSTICE MUST BE SERVED, NOW!!!”

“If this is not a direction to prosecute,” Dreeben said in court, “I’d really be at a loss to say what is.”

The night of that post, Trump said he would appoint Halligan, a White House aide without prior prosecutorial experience, as U.S. attorney for the Eastern District of Virginia, on an interim basis. She replaced a veteran prosecutor who was effectively forced from the job after not charging Comey or another Trump foe, New York Attorney General Letitia James.

Halligan secured an indictment of Comey days later as the statute of limitations on the case was about to expire. The charges are related to sworn testimony about whether Comey had authorized an FBI colleague to serve as an anonymous source to the news media.

Asked by Nachmanoff whether he considered Halligan to be a “stalking horse” or “puppet” for the administration, Dreeben demurred and opted against that characterization. But, he said, “She did what she was told to do."

Presidents, Dreeben said, have other tools at their disposal to punish critics, but bringing the full weight of the Justice Department to bear is impermissible.

“The government cannot use power of criminal prosecutions to attempt to silence a critic in violation of the First Amendment,” he said.

Lemons, the Justice Department prosecutor, insisted that Comey was indicted by a “properly constituted” grand jury because he broke the law — not because Trump ordered it.

“The defendant is not being put on trial for anything he said about the president,” Lemons said.

Lemons said nobody directed Halligan to prosecute Comey or seek his indictment.

“It was her decision and her decision only,” he added.

But Nachmanoff, the judge, noted that Trump appointed Halligan as acting U.S. attorney on Sept. 22, three days before she presented the Comey case to the grand jury.

“What independent evaluation could she have done in that time period?” he asked Lemons.

Nachmanoff asked Lemons whether he has seen a “declination memo” in which prosecutors had outlined reasons for not seeking an indictment against Comey. Lemons responded by saying that the department had instructed him not to disclose that “privileged” information.