Character mistake: 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.
Suggested correction: It's perfectly within character that Caffey wouldn't know this. He's been in the navy a short time, never tried a case in a courtroom, and is generally uninterested in military protocol.
Character mistake: Some of Colonel Jessup's ribbons are in the wrong order, and his Combat Action Ribbon is backwards.
Character mistake: When LTJG Kaffee says "whatever happened to saluting an officer when he leaves the room?" It's well known that Kaffee doesn't know much about military protocols, but Marines and Sailors do not salute while uncovered, especially indoors. Army/Air Force maybe, but not the Navy or Marine Corps.
Continuity mistake: Tom Cruise is sitting in the court room with his hands under the table. Quickly he moves them to the top of the table as he stands up. You see the glimmer of a wedding ring (when his character is single) and then the ring is gone. (01:08:00)
Visible crew/equipment: During the first credits, when the name Kevin Bacon appears on-screen there's a close-up shot of a bayonet. A white screen used for lighting and filming is perfectly visible reflected on the metal.
Continuity mistake: When Markinson gets in Lt. Caffey's car you can see his baseball glove on the back window ledge. Then in subsequent shots the glove sometimes missing.