Factual error: Lt. Caffey (Tom Cruise) wants the two marines to plead guilty and take a deal because he doesn't want the to "spend the rest of their lives in Leavenworth (prison)." The United States Disciplinary Barracks is indeed located in Leavenworth, Kansas. And the US Army and US Air Force send convicted felons there to do their time. However, Marines and members of the United States Navy are sent to Portsmouth Naval Prison in New Hampshire. It is run by the Marines.Nimzoman
Character mistake: During the trial, Danny says Lt. Col. Markinson shot himself in the mouth with a .45, but in the suicide scene, Markinson's gun is a Beretta 9mm, the standard-issue U.S. Military sidearm, and it is implied he shot himself in the left temple, not the mouth.