In early June, Attorney General Pam Bondi unveiled the indictment of Kilmar Armando Abrego Garcia, the immigrant mistakenly deported to El Salvador, with a pronouncement: “This is what American justice looks like.”

She predicted he would be easily convicted.

On Sunday night, 16 days later, a federal magistrate judge gave a far different assessment of the evidence presented so far: The department’s case had serious problems, relied heavily on deals with multiple informants, included dubious claims about his actions that bordered on “physical impossibility” and was rife with hearsay testimony.

The judge, Barbara D. Holmes, ordered Mr. Abrego Garcia to be released, but conceded he was likely to be detained for immigration violations as his case moves through the courts.

The decision to deny the department’s request to keep Mr. Abrego Garcia behind bars was hardly the final word about the criminal prosecution, nor was it a comprehensive or final reckoning about guilt or innocence. It was, nonetheless, the first time the charges have been subjected to judicial scrutiny and a blow to the government’s core contention that Mr. Abrego Garcia poses a danger to the community.

Although Judge Holmes did not mention Ms. Bondi by name, her 51-page ruling represented a rejection of efforts by top administration officials to publicly discredit Mr. Abrego Garcia by suggesting that he was a prominent member of the violent street gang MS-13, and that he trafficked women and minors.

Judicial rebukes have become commonplace in a conflict-courting administration run by a president intent on turning legal proceedings, including four recent criminal cases, into political mud fights.