Continuity mistake: The Time Worm comes out of the stick handle and is coiling around it to the left. The very next shot it is suddenly coiling to the right. (01:12:25)
Continuity mistake: The dragon on Jinx's shirt changes in size throughout the movie.
Continuity mistake: Serpentor's snake bites into Duke's chest on his left side. But when the doctor is treating him and he is lying on the ground, the wound is shown on his right side as Lt. Falcon walks up to him. It is back on his left side for the rest of the scene. (01:10:55)
Continuity mistake: The BET is shielded by a metal dome that folded up. Nemesis Enforcer walks up and peels two portions back to reveal it inside the dome. Two shots later from the side, the dome is suddenly completely gone on that side, despite Nemesis Enforcer only peeling back a little of it. (01:08:30)
Plot hole: After being hit with the spores, Cobra Commander cannot walk or even move very well with any speed at all. The Cobra minions have to drag him to their prison with the Joes and just leave him there on the ground after the Joes make a break for it. The Joes go quite a distance to engage Cobra. Road Block is delayed only a couple seconds behind the other Joes when he is grabbed, but knocks out the minion who grabbed him. Suddenly, Cobra Commander is at his feet telling him to wait because it's a trap. Later, Road Block has to carry Cobra Commander because he still can't move much. There's no way Cobra Commander could have caught up with Road Block to warn him of the trap. (00:52:50)
Continuity mistake: When Lt. Falcon is kicked out of the plane with a parachute, his hat blows off and is lost. He lands and fights "The Renegades" and meets Sergeant Slaughter, his hat still gone. When they drive off leaving him to walk, he pulls his hat out of thin air and puts it back on. (00:51:30)
Continuity mistake: After Lieutenant Falcon gets in trouble for bringing a date on base, the girl he brings is ordered away. She goes to a lake and strips off her white dress, showing off her one piece, and kicks the dress aside gently. In all the immediate shots following, when she's revealed as a Cobra agent and others are with her, the dress is nowhere to be seen. (00:33:10)
Factual error: The Joes chase Cobra into the snowy mountains and attack inside the weird cave. One of the Joe's vehicles splits to a driving section, and Road Block flying up in a little fighter. Road Block is holding a large rifle with both hands, yet the fighter goes up and turns around and begins flying at his control but he never touches a steering wheel or anything. Just his big gun. And he does not speak so no voice commands are given. How is he flying with no hands? (00:19:40)
Audio problem: When trying to steel the BET, Serpentor fllies in close and Duke grabs onto his glider. The sounds of TIE Fighters are used for Serpentor's glider. You can even hear Darth Vader breathing for a moment. (00:15:45)
Continuity mistake: In the opening battle sequence, Cobra Commander takes a bomb and sets it for 3:00 minutes. As he flies with his jet pack to the Statue of Liberty, it counts down to 2:58. He lands and places the bomb, and laser blasts hit all around him before he turns and flies off. This takes about 5 seconds to do, but the timer on the bomb stays at 2:58 for the full time of him landing, placing the bomb, and flying away. (00:01:35)
