But in this case, the decision to give the case to Mr. Machen’s office has left lingering concerns among some senior F.B.I. and Justice Department officials who worry that it was a mistake to entrust such a politically charged prosecution to an office with less experience than others in trying terrorists.

On Monday, Mr. Khattala, who will most likely go on trial this year or in early 2015, will make his first court appearance since his arraignment in June, and those doubts have not dissipated.

“This is not how it should have been done,” said one law enforcement official, who like others critical of the decision spoke on the condition of anonymity.

Another senior law enforcement official had a more specific concern.

“It took them nine months to charge this guy — far longer than it should have,” he said. “Initially, they just didn’t know what they were doing.”