Plot hole: Suzie pulls out some of her teeth with a pair of heavy pliers. This would leave conspicuous tool marks on the teeth that would be visible to the naked eye, let alone under forensic examination. The conclusion would be that Suzie is missing, not dead, and the whole plot would unravel from there.
Continuity mistake: Mr. Furlong pushes Zeke into the fishing tank and it breaks, soaking him from head to toe with water. Moments later they are walking out and he is dry.
Plot hole: The first time they communicate with the "entity" in the spaceship, they find a correspondence between numbers sent by the entity and letters of the alphabet. The entity presents itself as "Jerry". Later on, the entity tells Dustin Hoffman, "Stop calling me Jerry" - and then Dustin Hoffman realizes that the number-letter correspondence was wrong, and the actual name of the entity was "Harry". But if that is true, how could they have communicated without problems before? The very first word that the entity used was "hello", which would have to be displayed wrong, since it begins with an "h" and has an "e".
Continuity mistake: When Mulder and Scully start frantically running from the bees inside the dome Scully is clearly seen untying her belt twice. (01:01:55)
Revealing mistake: After the sniper is shot he falls through the wall. Look at his silencer when he hits the ground - it bends where it attaches to the muzzle. A real metal silencer wouldn't do that. (00:41:25)
Factual error: At the end when Ben Willis and his son have Julie at the graves, Ray shows up with a gun. He fires at Ben but there is no bullet in the chamber. Later after the fight between Ray and Ben's son Julie picks up the six-shot gun and fires 8 shots at Ben.
Continuity mistake: At the end, the paramedics are taking Samuel L. Jackson into an ambulance. His head is toward the front of the ambulance but in the next shot, Jackson's head is at the back of the ambulance. (02:08:25)
Other mistake: In the end credits, the filmmakers misspell the name of the town they wish to thank. They spell it "Coupville", but it's actually spelled "Coupeville."
Plot hole: During the end the murderer is thrown out the front window of the building. The students leave the building through the front door, but yet there is no body, and that doesn't seem to bother them!
Continuity mistake: When the Dude is in Jackie Treehorn's estate, he pencils over a pad of paper to see what Jackie wrote down while he was on the phone. He then hurriedly crumples up the piece of paper and shoves it in his wallet. Then, when we see the Chief of Police of Malibu looking through the contents of The Dude's wallet, the paper is there, neatly folded in fourths.
Continuity mistake: At the carnival, the glass of lemonade goes from half drunk to full. (00:32:20)
Continuity mistake: When Emma is protecting John at the top of the stairs and he says, "I didn't kill anyone," her hand is at her side. In the next shot, her arm is raised in front of him. One shot later, it's back at her side. (00:23:40)
Continuity mistake: In the picture of Morgan Moonscar in Simone's book, his scar is much longer than it was when we saw his ghost, and also later when we see his Zombie.
Continuity mistake: When Marcia Gay Harden is doing the final preparations for the party that night, she and Anthony Hopkins have a dialogue where they talk about favorites and children. Towards the end of the dialogue, she hugs him and the watch on her wrist says something like 10am. A minute later she hugs him again and the watch now says 12:25.
Continuity mistake: When the two girls are on the floor, just as the phone rings, Tomoko (the girl in green) has her right hand on Masami's (girl in red) shoulder. Cut to a different angle but now, Tomoko has her hand on Masami's arm instead of her shoulder.
Visible crew/equipment: About half the way through when Paul Newman is sitting on a seat in the police station with James Garner, the boom operator and another guy scratching his head can be seen to the left of Newman in the marble wall. It is fairly obvious taking up a 1/3rd of the screen. Also in the same time when Newman is walking through the halls of the police station with Stockard Channing a whole heap of movie posters can be seen on the walls like they used the offices of a movie studio as a police station.
Visible crew/equipment: When Marion is dead, you can see the camera panning back reflected in her eyes.
Visible crew/equipment: In scene where Chris is arguing with the cops look very closely in the window of the car. The boom mic, camera, and crew are all visible.
Continuity mistake: At the beginning of the film, Bill is shown coughing up the white gloves that had been stuffed completely in his mouth. However, later in the film, Cobb does not completely stuff the gloves in Bill's mouth.
Visible crew/equipment: When the ambulances and fire trucks show up at the building where the money was dropped off, the camera pans up the side of the closest ambulance and you can see the camera rig reflected in the windows. (00:34:55)