Deliberate mistake: The extras used in the scene when Danny gets assigned the case appear again as members of the jury. If Danny's colleagues were called as jury members for a trial all would have to declare a conflict of interest and be ineligible to hear the case. (00:09:30 - 01:03:25)
Continuity mistake: In the scene where Jo is telling Danny that she sent one of the prisoners some comic books (towards the beginning of the movie)he steps inside his car and the back window is halfway down. As he drives away it is completely up and as he pulls into the next scene, it is still up, while his driver side window remains down the whole time. (00:30:00 - 00:32:00)
Factual error: Danny is in his apartment watching a baseball game on TV between the San Diego Padres and the Atlanta Braves. The game announcer is Jerry Coleman for the San Diego Padres. Since Danny is in D.C., he would have been watching the game on WTBS TBS Superstation (an Atlanta TV station), and Jerry Coleman wouldn't have been announcing a San Diego Padres game on TBS. It would have been Atlanta announcers. (00:46:00)
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)
Continuity mistake: During Danny's drunken yelling scene he swoops a table ALMOST clear of its papers, meaning there are still a few papers messily left on the table. However, a few shots later, those papers are mysteriously missing. (01:47:20)
Continuity mistake: After Danny tells Jessep to sit back down on the witness stand and the judge is telling Danny how to address Jessep, he pours himself a glass of water. From the shot where his back is towards us he puts the pitcher down. We then see a shot in front of him and he is putting the pitcher down again. (01:56:00 - 01:58:00)
Continuity mistake: During the trial at the end, Jessup struggles with the MPs to get to Danny Kaffee. After the struggle, his tie is all out of place. In the following close-up shots, it's re-aligned, before becoming completely askew as Jessup goes to retrieve his hat.
Continuity mistake: In one scene when Sam and Jo are leaving Danny's apartment, there is a wide shot showing Daniel opening the door, then there is a close up of Daniel and Sam, and Sam opens the door again.
Continuity mistake: Near the end when Jack Nicholson is on the witness stand you can see his collar is wet from sweat, then after he gets up it is dry, then wet again...
Revealing mistake: In the scene where Tom Cruise is yelling at/questioning Dawson at the jail in the witness room, immediately after Cruise gets up in Dawson's face and says, "I'm the only friend you've got," Cruise is supposed to simply turn and walk away. But you can see from the angle behind Dawson that Cruise' first step is a step down, indicating that he was on a pedestal of some sort to bring their heights closer together.
Factual error: During the performance of the Marine Silent Drill Platoon at the very beginning of the movie, they are performing with Springfield 1903 Rifles, whereas the Marines perform with M1 Garands. The reason is that the Texas A&M Fish drill team was being used in the Marines' stead.
Character mistake: Some of Colonel Jessup's ribbons are in the wrong order, and his Combat Action Ribbon is backwards.
Continuity mistake: Part of Jack's opening statement has him walking towards the jurors with his left arm bent shot from behind the jurors. The next shot is from behind Jack, looking at the jury and his left arm is by his side.
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.
Suggested correction: It's likely Danny never knew the model of the gun that Markinson used. His point was to tell everyone (mainly the jury) that Markinson had committed suicide by shooting himself. Danny mentioning the model of the gun was not his point, he just did that for added effect.
Factual error: In the opening scene, during the overhead shots of the Marine band, the band members are out of step with the music. In military marching, the left foot ALWAYS falls on the downbeat of the music. In all other shots, the music is properly synchronised.
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.
Portsmouth has been closed since the 1970s. Left abandoned because it was too expensive to rebuild or demolish.
Continuity mistake: While having lunch outside, Jack Nicholson takes a cigar up to his mouth and when he is about to give a puff, shot cuts to a general view of him and now his arm is down and no trace of the cigar is seen.
Continuity mistake: Just before Danny sits down after questioning Mr. R.C. McGuire, look at his shadows on his jacket. As Jack gets up, notice the sun shadow on his jacket, it's at an angle, but Danny didn't have one.
Factual error: The film's presentation of Guantanamo Bay seems unrealistic. In an attempt to make Jessep seem autocratic and akin to a dictator, they show a scene of Jessep and Danny meeting outdoors. In the background, there is a colonial-era type mansion in immaculate condition. There are no such buildings on the Naval base at Guantanamo Bay.
Revealing mistake: In one scene, Tom Cruise is walking along the sidewalk with Kevin Pollak (who is pushing a pram). The camera, which obviously is moving backwards on a dolly, is in front of them. As the men walk past some bushes, watch the branch on the right-hand side. As it comes into view, we see it spring back and shake for a bit. Evidently, the camera dolly snagged it on the way past.