Plot hole: There must be a lot of dumb scientists in Sebastian's lab. While defibrillating the invisible gorilla, (s)he becomes completely visible for a moment. However, not once do the scientists consider that applying a mild electrical shock to the system renders the invisible animal visible again - that electricity may be the key to the whole invisibility problem. They don't even comment upon the fact that the gorilla does become visible.
Plot hole: Peter goes into Carl's mind to save Catherine. When he's in there he sees the tank with the water nymph. On the tank are strange symbols which provide the FBI with the clue needed to find the latest victim. Makes sense so far. But, go back to the scene just after the FBI have captured the comatose killer and are looking in his basement. The FBI are looking at the contraption that the killer uses to suspend himself over the victim. On the contraption is the same symbol seen later on the water nymph's tank. Why didn't the FBI follow up the symbol then?
Visible crew/equipment: In the scene after Patrick Bateman's second encounter with the detective in his office, we see Bateman having sex at Courtney's apartment. After he rolls off her, Bateman approaches the large, stand-up mirror in the bedroom. In the upper right hand corner of the mirror, a boom microphone can clearly be seen moving around to pick up Christian Bale's lines. The next time we get the same long shot, the microphone is gone. (00:52:45)
Other mistake: When Sugimura is looking for Kotohiki, he activates his scanner to see if she is nearby. The scanner shows her location, but fails to show either Mitsuko or Kiriyama, who show up quickly after.
Character mistake: At the memorial service the principal says that it's been 39 days since 39 loved ones had died. But there were 40 students on the plane and 4 chaperones, making the total 44. Now 7 people got off the plane, which means 37 people related to that memorial service actually died, not 39. Two pilots would make up the numbers, but there would be flight crew too, which still leaves the numbers off.
Continuity mistake: When Maya enters Peter's office for the first time, you can see that he had just written something on his laptop. While they talk, you can see the word-program on the computer screen: it shows one page. Cut to Maya, then back to Peter: it shows two pages. Another cut: one page. This happens two or three times throughout the scene. (00:29:30)
Revealing mistake: In the scene where Rudolph is saving Tony from the truck he says, "close your eyes, Tony". But in the next scene when they are on the blimp the boys introduce themselves. Rudolph did not yet know Tony's name but yet he said it.
Other mistake: In the beginning of the movie when Kimberly is shackled to the floor you can see that the padlock isn't locked. She could just take it off and be free.
Continuity mistake: When Harrison Ford is watching his wife laying in the bathtub ready to drown, the camera shoots her head several times between cutaways to Ford and the running water. Watch her head relative to the top of the tub in the various shots. In some her head is much higher than in others yet her body never moves.
Continuity mistake: When the Wiccan girl and the guy writing the book were sitting at the table the guy knocks down the cup when he hits the table. In the next shot the cup is up again.
Continuity mistake: When "B" accidentally pulls the leg off of the dead dog, the position of it in her hands changes between cuts.
Revealing mistake: Near the end when a naked John Jasper kills M, he staggers back and you can see a modesty pouch that is covering his private parts. (01:31:47)
Continuity mistake: In the scene in the mine, when the killer attacks the black guy, his miner's light is knocked off. A few seconds later when it switches back to him, he's wearing it again.
Continuity mistake: Several times through the film the Crocodile changes size from the size of a 30 foot croc to the size of a miniature barn.