Continuity mistake: When Tim and Lex first arrive, Lex is wearing a purple tank top with a colorful design, and in the following scenes or even between consecutive shots her tank top changes to completely different designs, though it's the same style of tank top.
Plot hole: The opaque red lined map that Otomo retrieves from his first fight is ridiculous. Why would people who know where the hidden base is be carrying around a map on them (which shows a route so basic that they'd have to be brain-dead not to be able to remember it anyway) just so that conveniently one of their enemies can get it?
Continuity mistake: When Simon Phoenix gets out of the sewer system (after gunning it out with the rebels and John Spartan) his left eye has the brown contact and his right eye has the blue one after going the entire movie with those contacts in the opposite eyes. (01:30:25)
Other mistake: In the scene at the beginning where Phil eats Jason's Heart, you'll notice that he screams like a monster for a bit. Don't you think that the two security guards would easily hear the screaming and intervene, being that they're in the very next room? (00:13:40)
Revealing mistake: While in the convenience store, watch the arcade screen the punks are playing, they are getting very excited about the game, however anyone who has played Street Fighter 2 will notice that they are merely looking at the demo version and even the words "insert coins" are displayed on the screen.
Continuity mistake: In one scene, Mark Hamill jumps into the passenger side of a car while running from men with guns; the men shoot at him, and the passenger side window is shattered by the gunfire. A moment later, once the car has gotten away, the passenger side window is intact.
Continuity mistake: When Mike Rogers's daughter is sleeping on his lap and his wife comes to ask him if he's coming to bed, in one shot the daughter is way up sleeping on his shoulder and in another, back down on his lap.
Continuity mistake: In the scene where Beldar has finished giving Gladys a driving lesson and they are sitting in the car, you can see that he has nothing on his lips. After Gladys kisses Beldar, you can see red lipstick. As the shots go from Beldar to Gladys and back, you can see the lipstick disappear and re-appear.
Plot hole: A nuclear armed stealth fighter is accidentally sent back in time to 1940's Nazi Germany. After the Nazis capture it, two days later they drop a nuclear bomb on the United States. There are several basic problems here. Firstly, if the Nazis captured advanced technology, wouldn't they spend more time taking the plane apart and interrogating the captured pilot? How on earth did they manage to train a pilot to fly the stealth in such a short length of time? And how did the stealth fighter manage to reach the U.S. from Germany when in-flight refuelling was unknown then?
Continuity mistake: After Bruce proposes to Andrea and he drops her off at home, she is wearing the ring on her left hand when she is inside his car. But once she steps out of it, the ring completely disappears.
Continuity mistake: In the scene where Gard telepathically fights an alien, you see his nose bleeding. Then the alien explodes, and in the next shot of Gard's face, the blood under his nose has vanished, only to return in the next shot of his face.
Revealing mistake: In the scene where Rick returns from the lab with the macaroons, it is obvious that the worm man is only in half of his costume. He's wearing black pants and shoes and sitting on a stool.
Factual error: Detective Beck's daughter states that she had not seen her father for several years. That he lived as a hermit and did not let her in. Then why when she goes with the good alien to where her father used to live, she has the key to get in?
Continuity mistake: The two buddies are eating and listening to the exposition news item about the "Zone of Personal Freedom." In the last part of the scene ("Who do you suppose are gonna call to clean that up?" the straw inside Chad McQueen's milkshake keeps swapping position between the middle and the rim of the glass. (00:03:20)