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)
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)
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)