ALEXANDRIA, Va. — The prosecution of former FBI Director James Comey hit another hurdle Wednesday as the Justice Department encountered mounting questions about how the case was presented to a grand jury for indictment.

The development 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 Justice Department’s acknowledgment under questioning from a judge that the full grand jury did not review a copy of th

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