Deliberate mistake: In the scene where they break into the train from its roof, you can notice that despite the high speed and the consistent wind, Captain America's fellows have no difficulties in running, standing up still, and even jumping, like they felt no air resistance. Moreover, you can see that their hair is not moving at all, completely missing to realize any "windy" effect.
Deliberate mistake: Polly's and Sky Captain's clothes are discarded because they are contaminated with uranium; however, Polly gets to keep her camera. Her camera would have been contaminated with uranium, too, because she had it with her in the underground cave.
Deliberate mistake: When Zoom is moving the documents from the desk to the floor for Marsha to pick up, she quite blatantly catches him two or three times, but continues on with her business.
Deliberate mistake: Elizabeth Shue uses a drawer handle as an electromagnet. OK if it's really a magnetic material but lab furniture is generally made of aluminium or stainless steel which is not. There is no way that they would use an iron handle in a potentially wet, and hence corrosive, environment such as a freezer.
Deliberate mistake: You might be wondering where Terry suddenly comes up with Jolly Jack all of the sudden after escaping the lab. In the commentary, they say that the Joker, in his transmission to Terry in the lab, was supposed to be eating out of a candy jar with "Jolly Jack" on it, but couldn't have it due to time constraints.
Deliberate mistake: During the scene where Carlos and L.J. are searching the motel, L.J. sees a zombie which turns out to be a reflection in a wall-length mirror. L.J. shoots, breaking the mirror and realizing his mistake. But, if he had been standing in front of the mirror as shown, he should have seen his own reflection standing there as well. This was done as an homage to a similar encounter in the original game. (00:24:20)
Deliberate mistake: When King Willie is confronted by the Predator in the alley the Predator approaches him cloaked stepping through the puddle of water. You can see his footsteps causing the water to splash up. However, you can see the water splash up and go through his foot. The Predator is only cloaked, not intangible so the water should have splashed upon his foot, not go through. Water against his foot would be visible too, even though he is cloaked. (00:47:45)
Deliberate mistake: After Wolverine arrives at 3 Mile Island he approaches through a thick fog. Above him are a series of conveyor belts that are used at a coal power plant, not a nuclear plant such as 3 Mile Island. The belts are unique to coal mines and coal power plants, and would not be found at a nuclear power plant. The filmmakers obviously couldn't film on the site of a nuclear plant, so filmed on a coal plant to fill in.
Deliberate mistake: The Stan Lee cameo contains a factual error; he's checking out of the Mallrats script and rehearses his lines, but despite coming out later in the year, the movie (and therefore Lee's cameo) had already been filmed, since movie shooting ended in April. Unless we have to assume Stan Lee carried with him all the time scripts of movies he'd been in and randomly read his scenes aloud. (00:30:45)
Deliberate mistake: During the space battle, one of Drax's men gets his back pack blasted. (1:46:37) His entire pack explodes so that his jet pack and life support are destroyed. But as a result of that blast, all the parts from his suit FALL DOWN! Even though there's no gravity.
Deliberate mistake: The shots of the prisoner skiff during the transport to the Sarlacc Pit are reversed. This can, for example, be seen as Chewie's bandolier is on the wrong side, and that Han's shirt is overlaying the wrong way.
Deliberate mistake: During the opening shot and titles, Neville is shown driving by the same block three times, each from a different angle. The first shot is high, the second shot (00:01:50) is from the hood of the car looking at Neville, and the third (00:02:40) is ground level.
Deliberate mistake: The turn count for Lisa's stay in the Cryogenic Sleep Chamber is off. The card reads she should be there for 5 turns. 'Turn' can either represent a single move made by either Danny or Walter, or a complete game cycle where both Danny and Walter have made a move. If we count the turns by player, it comes to 8 and she's awake 2 turns too late as it should have happened at the start of 6th. If we count both players' moves together as a start of a turn, then she's awake 2 turns too early as its turn 4 and not turn 6. It seems obvious from showing us the shower suddenly start up that this is the correct point in the film they wanted her awake, so it's unlikely she was actually awake off-camera during the Astronaut's arrival and we just didn't see.
Deliberate mistake: O'Niel needs a sample of a dead man's blood to test for toxic drugs. So he visits the corpse, which has been dead for quite some time and is lying on its back, and proceeds to insert a hypodermic syringe into the dead man's frontal neck, extracting the sample. But blood pools low in the body soon after death. There ought to have been no blood available from that location of the body. To get blood, O'Niel should've punctured the corpse's underside.
Deliberate mistake: When Alice first fights the Nemesis, she attempts to jump over a fence and make an escape. When she lands on the police car, Nemesis fires his RPG at her. If you look closely, the rocket passes magically right through a chain link fence without touching it at all. (00:44:40)
Suggested correction: Rocket made a big hole in the mesh. Clearly shown.
Deliberate mistake: In the end sequence, when the joyous Valley of the Wind people run past Yuppa and the old woman to welcome back Nausicaä among the living, the same group(s) of people are seen twice running from the right to the left.
Deliberate mistake: There's a bizarre editing gaff in the opening fight of the Director's Cut. At one point, Fasil's sword vanishes (for no real reason) and he starts to do backflips. The scene then cuts away, and when it cuts back, he's suddenly running and has his sword again. A few shots later, he's suddenly doing backflips and has lost his sword again. (It's meant to be Fasil doing the flips.) The editing makes absolutely no sense. It's like they somehow mixed up two different scenes during editing.
Deliberate mistake: In the Director's Cut (the version most readily available on DVD), there is literally an entire 15-second chunk of the final fight that is repeated twice within 60 seconds. (It's the bit where Duncan and Kell are fighting on the ground, Duncan kicks Kell, then Kell kicks and slices Duncan) It's impossible not to notice, and it's not they're flashing back to what just happened... they just repeat the same 15 seconds of footage, add different sound effects, and assume people won't notice.
Deliberate mistake: It's not particularly believable that the away team to stop the assassination would consist of the ship's entire senior staff, and raises the question of who was left in charge of the bridge (the answer: apparently nobody, as they return to a completely deserted bridge). Of course this is dramatic license, and at this point the audience won't care or likely even notice.
Deliberate mistake: When Hellboy is attacked by the spider-lady, as the spiders begin to descend on him to steal the sword, you can easily tell that some of the shots of the spiders coming down are repeated 2 or even 3 times, and simply flopped horizontally to appear different.