The scars on Sara's forehead and cheek keep vanishing and reappearing on different sides of her face, and are all completely gone by the end of the film.
(at around 30 mins) When Price takes them all to the casket to get the guns, one of the windows is not shuttered yet "lockdown" had already happened.
(at around 47 mins) When Melissa Margaret Marr first screams, she screams when she sees the ghost. When everyone looks over her tape, she screams when the ghost takes her into the house.
(at around 33 mins) When Pritchett, Sara and Eddie are first in the basement, and Sara give the torch to Pritchett. You see him raise his hands in the air, and neither of them shows any evidence of the cuts he sustained while breaking the glass in an earlier scene.
(at around 1h 27 mins) At the end, when the two look at the million dollar cashier checks, all five documents have the same serial number.
(at around 30 mins) The characters claim they cannot tell if their pistols are really loaded because the magazines are "welded" into place. First, the pistols are all Sig Sauer P228 9mm which have plastic magazine wells which wouldn't be "welded." Second, like all semi automatic pistols, the shells can be manually unloaded via the slide, and can even be fully disassembled without any need to access the magazine well.
At 1:10 Evelyn betrays Blackburn and stabs him repeatedly. When she throws the weapon to the floor it is clearly a folding straight razor, useful for slashing but useless for stabbing.
The movie is set in the present yet when the hospital was shut down in 1931, electroconvulsive therapy (electro-shock treatment) was not yet administered. It wouldn't be until 1937 which it was first used.
Some of the warnings in the basement are in very bad German - it seems somebody just used a dictionary and translated the English lines word-for-word. For example, one sign has the phrase "Steh zurück!" which means something like "Stay back!". A correct translation would be "Zurückbleiben" or in this context "Eintritt verboten" ("No admittance").
(at around 4 mins) When Dr. Vannacutt is about to begin cutting open the patient you can clearly see the patient's left wrist slip out of the wrist restraints, but continues to act strapped in.
Several times during the movie, a character cocks a gun and the click of a gun being cocked is heard, but each time, the gun the actor is holding is shown with the hammer in the decocked position.
(at around 20 mins) When the camera tracks in on Schecter in the control room in the haunted house, there are two very conspicuously CG-added Blockbuster video boxes under some paper. They wobble as the camera moves closer to them.
(at around 46 mins) When Melissa goes to the basement with her camera and her camera starts to show the ghosts performing an operation, it is an obvious recording as the camera begins to pan on the video before the actress moves the camera.
When the characters hear the lock-down mechanism kick in, no one knows what it is, but Pritchett, who is only about twenty feet from the entryway, looks up and makes a mad dash for the entryway. There's a few shots of the characters watching the steel shutters slam into place as the structure seals up with the entry way the last egress to fall into place. Given that Pritchett was already running at the start of the process and was in close proximity to the entrance, he should have easily escaped the lock-down instead of getting trapped inside with the others.
The hospital was closed in 1931 yet much of it is lit with fluorescent tube lighting. Fluorescent tube lighting was not in commercial production until the late 1930's and not in widespread use until WWII.
(at around 1h 27 mins) The film is set in L.A. At the end of the movie, the sun is shown rising over the ocean (some have argued that the time is uncertain and that it could just as easily be sunset).
(at around 36 mins) When Eddie and Sara walk into the Zoetrope room, the mic is visible at the top right of the screen, peeking out from behind the zoetrope tank. Eddie's flashlight shines right on it at one point.
(at around 1h 12 mins) At the beginning Sara introduces herself as Jennifer Jensen, but later on when she is looking for Melissa Marr just before shooting Price she is calling out to her saying, "It's Sara." But she only revealed that she is Sara while talking to herself.
Geoffrey Rush's character is named Stephen Price, but on the invitations the guests read, his name is spelled Steven.