Continuity mistake: As Hermione walks toward the troll, just before she asks, "Is it dead?" the long towel hanging from the rod beside the sinks is visibly straight. When Harry lifts his wand with troll booger/bogey, in the shot of him as he grimaces and groans, the towel on the rod is visible behind him and it's messy. Yet when McGonagall, Snape and Quirrell walk in, the long towel is straight again.
Picture edited by Super Grover
Continuity mistake: After Gerry gets smacked in the face by the 'broken' suspender clasp, we see the silver clasp land under the dresser. Yet, when he's moaning and lifting his leg to get onto the bed, we can actually see the clasp still intact on the front suspender that came loose, which is dangling right behind him (just look between his legs). Of course, in the next shot, that clasp is gone. Since the silver clasp is one of the plot points, this is bizarre to say the least.
Continuity mistake: When John and Catherine are in the hangar at the runway, the Cessna's tail number is N3035C. When the plane is shown in the air, the number is N3973F. When they land, the tail number has changed back to N3035C.
Continuity mistake: In the bedroom scene the girl is holding a clear cup full of beer. The camera goes off her and when it comes back she is holding a blue cup. The camera goes back off her then on her and the cup is clear again. [This mistake does not appear in the unrated version - the blue cup scenes were shot specifically to secure an R rating from the MPAA because the contents are obscured.].
Continuity mistake: When Sam is in his bedroom, after he finds the Cube sliver it falls and dramatically burns a hole through the floor into the kitchen. But Sam's bedroom is over the living room (there is nothing on the ground floor below Sam's elevated bathroom, and in the first movie Jazz hides in this open space), and the kitchen is actually located between the den and dining room, at the other end of the house. If they were to follow the actual floor plan of the house, the Cube sliver would have landed in the area of the piano in the living room, but where would the fun have been in that?
Continuity mistake: When Mae videos phones Annie, she rotates the phone to a landscape position, and has her hand along the top of the phone. Once the call has been made, she lowers the phone slightly, and moves her hand from the top of the phone, to along the side. The shot then cuts to the phone, and her hand is suddenly along the top of the phone again.
Continuity mistake: When Pierce first begins to interrogate Caliban in the safe house in Mexico, a large portion of Caliban's albino makeup is smudged below his nose, revealing the actor's natural skin in his first close-up of the scene; after switching to a close-up of Pierce, then back to Caliban, the smudge has been fixed.
Plot hole: The film makes many references to the previous films and TV series as evidence of Batman's desire to be alone, but in the TV show and two of the films Robin has been established as his sidekick already.