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?
Continuity mistake: William H. Macy makes dinner plans with the Mayor and writes "Dinner with the Mayor" on the dry erase board in his office. He writes "Dinner w/ the Mayor" in the "Tuesday" slot. Then an intern comes in and accidentally wipes the appointment off the board with her shirt. Macy yells at her and tells her to rewrite the appointment on the board. The whole premise of the joke and pretty big part of the movie is that the intern rewrites the appointment in the wrong day, thereby causing the Hollywood people to miss dinner, enrage the Mayor and his wife and have the town turn on them. When the girl walks away however, the appointment is clearly rewritten in the correct day (Tuesday). This ruins the whole misunderstanding because although the appointment is in the wrong day later in the movie, at the moment the joke is supposed to be set in motion, there is no mistake.
Continuity mistake: In one of the opening scenes when Bob comes in from walking the dog in the rain, he dries the dog off with a towel and puts the towel on top of the coat tree. He tries to feed the dog and when it cuts back to the dog the towel is on the floor, then his wife comes in and the towel is back on the coat tree.
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)
Continuity mistake: Ben Affleck has a large tattoo on his right shoulder/bicep that has been covered up by make-up for the movie. During the 'waterpark' scene Ben is wearing a T-shirt and when he scoops the little boy out of the water and lifts him into the air the sleeve of his shirt pulls back a little and you can clearly see the bottom of his armband tattoo.
Factual error: Gary Sinise looks at a computer screen with a short section (about two full twists) of DNA on it and proclaims that "This DNA looks human." He could have been looking at DNA from any single-celled organism and it would have looked just as human as what he was looking at. All mammals have 90+ percent of their DNA in common, he would have to have sequenced the entire DNA strand (something like 3 billion pairs of nucleotides) to identify it as human, something that would be totally beyond the capacity of anything but a well-equipped genetics lab, something they show no sign of having.
Factual error: When John Cusack puts Springsteen on his LP-player, he places the needle at the start of the record. The song that plays is the studio version of "The River." Therefore, the album has to be "The River," which is a double album, but "The River" is not at the start of either of the two LPs, but is the last song on LP #1. (00:18:10)