Revealing mistake: When Linderman dashes at Jason and impales him with an American flag, Will is dragging Lori (who is supposed to be unconscious). He's dragging Lori by her arms... but when he suddenly reaches behind his back with his right arm, her right arm stays up in the air. (01:13:50)
Continuity mistake: As Viktor's tomb is opening there is a shot from above showing Selene looking down the opening tomb. Watch the placement of her feet. In the next shot, her feet have moved closer to the opening. (00:44:40)
Revealing mistake: When the camera shows the coffee cup in the cop's car, you can see the ignition is in the off position. (00:09:16)
Continuity mistake: In the scene where the Sheriff is wrapping the suicide victim's body, he has a roll of plastic wrap. He is shown with the box, then as he begins to wrap the head, he has just the roll, and in the next shot it is back in the box again. He presumably would have left it out of the box the entire time, since the box would only get in the way of trying to wrap the body. (00:33:00)
Visible crew/equipment: When Scott falls after getting hit by the three arrows, you can clearly see a long tube leading all the way up his leg which pumps the fake blood up to his shirt. (00:41:25)
Revealing mistake: Near the end of the film when we see Rhodes shoot Larry in the chest, you can see an outline of something underneath his vest, very obviously a device/squib simulating being shot in the chest. (01:15:15)
Character mistake: The very advanced computer on the plane can't spell, since it infers probabilities that a member of the crew has been "INFECTETED" by the creature. (01:06:40)