WASHINGTON — The federal judge presiding over the classified documents case against former President Donald Trump and two of his associates denied a request Monday to dismiss some of the charges in the indictment.

But U.S. District Judge Aileen Cannon did agree to strike a paragraph from the indictment that defense lawyers said was prejudicial and included information that was not essential to the underlying charges. The paragraph concerned allegations that Trump showed a classified map of a foreign country to a representative of his political action committee while discussing a military operation.

She left the rest of the indictment intact for now while also chiding special counsel Jack Smith’s team for having included in charging documents language that is “legally unnecessary to serve the function of an indictment” and for creating “arguable confusion” in the allegations.

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The motion to dismiss the counts is one of multiple pretrial requests and disputes that for months have piled up before Cannon, snarling the progress of the case and prompting the judge last month to indefinitely postpone a trial that had been set for May 20 in Fort Pierce, Fla. She has scheduled additional arguments for later this month, including on a Trump challenge to the legality and funding of the Justice Department’s appointment of Smith as special counsel last year.

The delays are all the more startling given that many legal experts had seen the classified documents case as exceedingly straightforward in its allegations that Trump had illegally hoarded classified documents from his presidency at his Mar-a-Lago estate in Palm Beach, Fla., and obstructed FBI efforts to get them back.

The defendants in this particular motion had sought to throw out more than a half-dozen of the 41 counts in the indictment, which also accuses Trump of conspiring with valet Walt Nauta and Mar-a-Lago property manager Carlos De Oliveira to conceal the sensitive files from the government.

The defendants had challenged counts related to obstruction and false statements, but Cannon said in an order Monday that “the identified deficiencies, even if generating some arguable confusion, are either permitted by law, raise evidentiary challenges not appropriate for disposition at this juncture, and/or do not require dismissal even if technically deficient, so long as the jury is instructed appropriately and presented with adequate verdict forms as to each Defendants’ alleged conduct.”

Cannon has already rejected multiple other motions to dismiss the case, including one that suggested that Trump was authorized under a statute known as the Presidential Records Act to keep the documents with him after he left the White House and to designate them as his personal files.