WASHINGTON (AP) — The Justice Department engaged in a “disturbing pattern of profound investigative missteps” in the process of securing an indictment against former FBI Director James Comey, a federal judge ruled Monday in directing prosecutors to produce to defense lawyers all grand jury materials from the case.

Those problems, wrote Magistrate Judge William Fitzpatrick, include “fundamental misstatements of the law” by a prosecutor to the grand jury that indicted Comey in September, the use of potentially privileged communications during the investigation and unexplained irregularities in the transcript of the grand jury proceedings.

“The Court recognizes that the relief sought by the defense is rarely granted,” Fitzpatrick wrote “However, the record points to a disturbing pattern of profound investigative missteps, missteps that led an FBI agent and a prosecutor to potentially undermine the integrity of the grand jury proceeding.”

The 24-page opinion is the most blistering assessment yet by a judge of the Justice Department’s actions leading up to the Comey indictment. That case, along with a separate prosecution of New York Attorney General Letitia James, have stirred concerns that the Justice Department is being weaponized to pursue President Donald Trump’s political opponents.

Both defendants have filed multiple motions to dismiss the cases against them before trial, arguing that the prosecutions are improperly vindictive and that the prosecutor who filed the charges, Lindsey Halligan, was illegally appointed.

Comey’s lawyers had sought the grand jury materials out of concerns that irregularities in the process may have tainted the case. The sole prosecutor who defense lawyers say presented the case to the grand jury was Halligan, a former White House aide with no prior prosecutorial experience who was appointed just days earlier to the job of interim U.S. attorney for the Eastern District of Virginia.

Fitzpatrick had earlier this month directed prosecutors to give the defense grand jury materials, but was then directed by the trial court to examine the matter further. In his order Monday, Fitzpatrick said that after reviewing the grand jury proceedings himself, he had come away deeply concerned about the integrity of the case.

“Here, the procedural and substantive irregularities that occurred before the grand jury, and the manner in which evidence presented to the grand jury was collected and used, may rise to the level of government misconduct resulting in prejudice to Mr. Comey,” Fitzpatrick said.

Halligan did not immediately return a message seeking comment and a spokesman for the office declined to comment.

Fitzpatrick listed among the irregularities two different comments that a prosecutor — presumably, Halligan — made to the grand jury that he said represented “fundamental misstatements of the law.” The actual statements are blacked out, but Fitzpatrick said the prosecutor seems to have ignored the fact that grand jurors cannot make a negative inference about a person who, like Comey, exercised a constitutional right to not testify.

The judge also raised concerns that the transcript of the grand jury proceedings was incomplete.

The two-count indictment charges Comey with lying to Congress in September 2020 when he suggested under questioning that he had not authorized FBI leaks of information to the news media. His lawyers say the question he was responding to was vague and confusing but that the answer he gave to the Senate Judiciary Committee was true.

The line of questioning from Sen. Ted Cruz appeared to focus on whether Comey had authorized his former deputy director, Andrew McCabe, to speak with the news media. But since the indictment, prosecutors have made clear that their indictment centers on allegations that Comey permitted a separate person, a close friend and Columbia University law professor, Dan Richman to serve as an anonymous source in interactions with reporters.