The federal prosecutor was frustrated. She was meeting with a grand jury in Chicago in October, trying yet again to secure an indictment for the Department of Justice in a case against protesters arrested during the Trump administration’s immigration crackdown. The jurors, peppering her with questions during the secret proceedings, were not convinced.

“I heard this case like last week and I thought it was a crock,” one of the grand jurors told the prosecutor, Sheri H. Mecklenburg, adding a profanity. At another point, a grand juror asked whether the government could “have unlimited tries” in bringing the same case before them. “Like you keep coming back as many times as you want?”

Transcripts of the exchanges, which a judge on Tuesday took the unusual step of releasing after a request from the defense teams, revealed potential breaches of protocol by the prosecutor in Chicago, part of a pattern in which judges have castigated government lawyers for missteps and courtroom tactics. Across the country, federal prosecutions have stalled before skeptical grand juries, which have been reluctant to indict based on the evidence presented to them.

While resubmitting a failed case to a grand jury is permissible, it was rare before the Trump administration, legal experts said. According to the Justice Department manual, seeking an indictment after a grand jury has turned it down requires the approval of the U.S. attorney overseeing the matter.

Nearly 200 pages of transcripts were released after hearings in which Judge April M. Perry questioned the conduct of the federal prosecutors who had presented the case against six people who had been arrested while protesting at a federal immigration detention site near Chicago last fall.

Prosecutors asserted that protesters had banged on a federal vehicle that was attempting to enter the detention site, and proceeded to block it, push against it and damage a side mirror and a windshield wiper. After initially failing to get an indictment, the government eventually persuaded a grand jury to indict the protesters on charges of interfering with a federal agent and conspiring to interfere with an agent.

The government’s case imploded: All charges were dropped after Judge Perry uncovered errors by prosecutors during the grand jury process.

“Your sole goal is to do justice,” Judge Perry told Andrew S. Boutros, the U.S. attorney for the Northern District of Illinois, last month. She added later, “That trust has been broken.”

The newly released transcripts raised additional questions of professional conduct.

Prosecutors are not permitted to vouch for the veracity of charges under standard legal protocols, but Ms. Mecklenburg told grand jurors at one point, “you know me and you trust me, and I would never ask you to charge somebody if I didn’t think there was probable cause.”

Ms. Mecklenburg made her feelings plain, telling one grand jury member: “I’m feeling the skepticism already. Are you going to be able to listen with an open mind?” At another point, she said she was “disappointed that there are people who didn’t want to hear” from a witness.

Mr. Boutros, who was appointed to lead the Chicago office last year by the Trump administration, apologized to Judge Perry last month and said that he addressed the conduct of prosecutors in the protesters’ case as soon as he learned of it.

Mr. Boutros has been the focus of criticism in recent weeks for his handling of the office, from which dozens of prosecutors have departed in the past year, including much of the office’s senior staff. On Monday, more than 100 former federal prosecutors, including a former U.S. attorney in Chicago, signed a letter citing a “failure of leadership” in the office and urged Mr. Boutros to “stand above and apart from political fealty.”

Mr. Boutros’s office is overseeing a criminal investigation related to E. Jean Carroll, a former magazine writer who accused Mr. Trump of sexual assault in New York City. That investigation into the funding behind Ms. Carroll’s successful lawsuits against Mr. Trump has drawn many critics, who note that it comes amid the president’s repeated calls for retribution.

Joseph Fitzpatrick, a spokesman for Mr. Boutros and for Ms. Mecklenburg’s office, declined to comment on the release of the transcripts.

Christopher Parente, a lawyer for one of the defendants, said that the transcripts show that the case was a “sham political indictment.”

“The Department of Justice attorneys involved in this case refused to accept that reality or their constitutional obligations, committing appalling misconduct and putting their D.O.J. marching orders above justice,” he said.

Todd Blanche, the acting attorney general, defended Mr. Boutros in a social media post last week, saying that the Justice Department “fully supports U.S. Attorney Boutros and his efforts to combat violent crime, drug trafficking, immigration violations, and fraud, and we look forward to more great work from his office.”