Continuity mistake: When the car door is ripped off by the cow, it shows the truck with the door intact.
Other mistake: When everyone is looking for Bobby, Matthew Lillard says that it is no use shouting because the glass is 100% sound proof. Yet when he is trapped in the cage, he hears Maggie screaming directions for him to dodge the ghost - not sound proof at all then.
Continuity mistake: When chasing Jamie in the woods, Mikey's headlights go from normal chevy headlights to off-road high beams.
Continuity mistake: In the scene where the Nemesis kills the 13 S.T.A.R.S members, after it blows up the sniper on the roof an additional S.T.A.R.S member can be seen outside the building on the right who wasn't there earlier. He then disappears shortly afterwards.
Other mistake: When Lawrence is looking at his wound in the mirror, it has slightly healed. Later, when Sir John visits Lawrence in the asylum, he shows the bite mark he got from the feral child to Lawrence. Since Sir John is also a werewolf, the bite mark should not be there.
Continuity mistake: When Sister Irene's habit is ripped at the back, you can see a bra strap on her left shoulder which disappears when she is seen at the front and when the camera is closer to her back (when she has the pentagram carved into her).
Continuity mistake: In the scene where Jonathan picks up the scarab, it breaks open and the beetle inside starts to crawl under his skin. We see Brendan Fraser tear Jonathan's shirt and cut the beetle out of him. However, in the very next scene, we see Jonathan walking into the temple, his shirt is intact and there is no blood to be seen. (01:37:05 - 01:38:30)
Plot hole: When Alex and Clear are sitting and having coffee they are on a corner. He looks in the window to see the bus pass, and as he looks to see if it is there, it's not. As the camera pans across the street, there is some construction going on which is blocking that whole road from being used, but then Terry, Carter's girlfriend gets "waxed" by the bus - no way it could have got through all that construction.
Visible crew/equipment: When Ashley is running down the corridors before escaping back into her medical room, you can see the dolly that The Engineer chasing her is being pushed on. (01:04:50)
Revealing mistake: When John Cusack is driving the actress, there is a shot looking over his right shoulder at the dashboard. The speedometer reads 0 mph. (00:08:15)
Deliberate mistake: At the beginning and especially at the end, Julianna Margulies spends extensive time in the ocean, wearing nothing but cargo pants and a T-shirt. Considering the movie takes place just off the Bering Strait, wouldn't she have quickly frozen to death? (01:21:05)
Character mistake: When they're on the island and the INGen helicopters are flying in, Jeff Goldblum takes the binoculars and looks through the wrong end. (00:32:30)
Other mistake: After Michael kills Laurie at the beginning, he hands the knife to the inmate with the clown mask. The next kill is the cameraman for which he uses the tripod ends. A few scenes later they show Michael standing holding a knife with fresh blood on it. He hasn't killed anybody with this knife yet so where did the blood come from?
Visible crew/equipment: At the start of the film, just after the war exercise, when the Sergeant begins yelling at the recruits you can see the outline of his microphone under his T-Shirt. (It's not his dog tags because you can see the shape and dog tags are not shaped like that.)
Revealing mistake: When Charley stabs Dandridge in the hand with his pencil, he stabs the hand holding him by the neck. The depth of the wound on Dandridge's hand reveals that the pencil should have stabbed Charlie in his neck and given him a severe wound, if not kill him.
Deliberate mistake: In the final shot of the film, Jill's head moves slightly when she's supposed to be dead. In the commentary, Wes Craven confirmed this wasn't strictly intentional, but he decided to leave the take in on purpose in case he decided to bring her back in a future installment. But unless a sequel proves she's still alive, it's technically a mistake, albeit a deliberate one.
Continuity mistake: When Mommie is cutting Christina's hair it keeps on changing from long to short several times.
Continuity mistake: At the start of the film, the dog is seen going from room to room looking for food. Just before he goes into Dana's room, someone can be seen through the crack in the door, moving from left to right.
Continuity mistake: James takes off his tie to cover the cut on Kristen's hand, but when they run outside to escape in the car James is wearing his tie again, then after the failed escape they run back inside the house and James tie is missing. In another scene Kristen goes into the woods to look for James and falls into a ditch, then as she climbs out the tie is missing from her hand, but the next scene it's back in place.