Deliberate mistake: The prisoners in the dark dungeon would not be able to read the letter (to Miss Dudley from Jason Flemyng that the carrier pigeon had) or see such a clear reflection by pouring water on the stone floor and holding the letter (written backwards) by the water. The room was suddenly lighter when doing so, but it wasn't clear where the light was coming from. Also, sunlight coming through the small window would not beam straight down along the wall. (00:07:23)
Audio problem: The FBI agent is in pursuit of a suspect in a hospital, once he enters the stairwell he draws his Glock handgun, and a click can be heard for a safety disengaging. Glocks are striker fired, they contain no external safeties that can be manipulated that would cause a sound. A sound can also be heard after the gun is already drawn from the holster, representing a holster draw sound. (00:22:22)
Continuity mistake: Xiao Meng spent some time wrapping her father's (Professor Tao) left hand, going around his wrist/thumb and under his thumb (diagonally across his palm). When Tao was blown off the bridge and landed in the dirt, the bandage was NOT wrapped around his thumb (just around his wrist). (01:12:33 - 01:16:03)
Other mistake: Throughout this, a running gag is that Fred can't drive stick/clutch. However, in "What's New, Scooby-Doo?" Series 2, Episode 6 "A Scooby-Doo Halloween," he yells at Shaggy that he's riding the clutch too hard at the beginning of the episode. If the Mystery Machine has a clutch mechanism, he would know how to drive stick/clutch.
Continuity mistake: When Nicolas Cage aka Frank Walsh first shoots a blow dart at Kevin Durand aka Richard Loffler he hits him in the left shoulder. Ten seconds later Kevin he pulls the dart out of his right shoulder. (01:23:15)
Revealing mistake: Obvious use of green screen for buildings across the street. On and off, the background fades, and buildings appear higher or lower depending on the camera's angle. At one point, the angle of walls behind Rex (Bruce Willis) is at a downward angle, and his head is almost touching the ceiling. (00:06:10 - 00:07:25)
Plot hole: SPOILER ALERT! During the final fight, Joey kills Frank and she reverts back to human form. Abigail tells her she's fine, because Frank was the one who turned her. However, when Frank kills Lambert he does not revert back to human form, even though Lambert was the one who turned him.
Continuity mistake: When the guy leaves the motel, he only grabs his jacket, but when he's outside, he has a helmet in his hand. (01:14:55)
Continuity mistake: At the beginning of the movie, the girl gets assaulted from the back: you see at first exactly from the shot from behind that the backpack she is carrying escapes her arms, but in the subsequent shot she is still holding it. (00:02:10)