The Lindsey Halligan-led prosecution of James Comey faced its latest rebuke Wednesday, when a federal judge said the government had taken an “indict first, investigate second” approach. It wasn’t the first time a judge has cast doubt on the Justice Department’s conduct in the case, still in its infancy, and it’s unlikely to be the last.

The critique came from U.S. Magistrate Judge William Fitzpatrick during a hearing in Virginia over the handling of evidence in the case brought by Halligan, whom the Trump administration installed to secure the indictment against the former FBI director over the objection of career prosecutors. The New York Times reported that the judge “seemed exasperated with the government’s approach, described the case as ‘unusual’” and said, “We are in a little bit of a posture of indict first, investigate second.” The judge ordered the prosecution to turn over grand jury materials by Thursday.....

Last month, the main jurist presiding over the Comey case in Virginia, U.S. District Judge Michael Nachmanoff, rejected the DOJ’s motion for a protective order that, he wrote, “would unnecessarily hinder and delay Defendant’s ability to adequately prepare for trial.”

It’s unclear if a trial will be necessary to resolve the case, which was prompted by Trump’s explicit demand. Comey’s challenge to the legality of Halligan’s appointment could lead to the case’s dismissal pretrial, as could his motion to dismiss based on vindictive prosecution and other issues. While rulings on those big issues are still pending — and we should learn more later this month on how they might fare — these initial stumbles don’t bode well for the prosecution.