Other mistake: The shot showing the vault swinging back to his location is the same that the one where the vault is swinging out, but going backwards.
Character mistake: When Bruce is looking at Chase's various clippings of Batman on her desk while she's tending to the tea kettle, there is a paper that says "Diagnosis Form #39," and just above it, the word "schizophrenic" is incorrectly spelled as either "schizofrenic" or "schizoprenic" (a metal clip is partially covering the last six letters of the word, so it's hard to determine whether it's an "f" or a lone "p" where the "ph" should be). (01:03:11 - 01:03:32)
Continuity mistake: When Bruce is at Dr. Meridians place, Bruce receives a call from Alfred. Bruce moves his finger on the side of the communication device up. The next shot shows him doing it again. (01:02:05)
Continuity mistake: In the fight scene outside the elevator at the beginning of the movie, there are at least two shots where you see Batman's back without his cape in the way. There are no items whatsoever attached to the back of his belt. Subsequently he manages to pull the stun device and the grappling gun with grappling hook from behind his costume. A previous corrector proposed that the devices could not be seen because they are concealed in "pouches" on Batman's belt. Close inspection of the scene shows that there are no pouches of any kind on his back or concealed in his cape.
Continuity mistake: In the vault, just before Batman enters, we get a nice shot of the bank guard. He appears to be lying length-wise in the vault, his body flat and straight, and his head laying on the "step" toward the left side of the screen. When the scene cuts to Batman entering the vault, the guard is positioned differently, at much more of an angle, and his head is higher, closer to the second row of boxes from the bottom of the vault. (00:07:25)
Revealing mistake: When Dr. Meridian first drops out of the tube, her skirt flies up. However, when she is falling in the shaft, her skirt is down and barely moving. (01:46:55)
Continuity mistake: In the part after The Riddler shows Two-Face the newspaper with the headline "Batman Survives Subway Sabotage," The Riddler pushes a glowing green cylinder into the monkey's mouth and the camera cuts to the screen so they can see Bruce Wayne's brain. When it cuts back to Two-Face and The Riddler, the cylinder isn't there. (01:25:54)
Visible crew/equipment: To escape Two-Face's ambush, Batman tilts the batmobile onto its rear wheels, and thanks to the bat-hook, he's able to use the vertical facade of a building as an alternate route. As the batmobile rides up the building, if you look closely you can see what looks to be a wire behind the batmobile (probably helping the batmobile or a model of it travel smoothly up the building or a model of the building). (00:50:35)
Continuity mistake: After the Bat-Boat is destroyed, it changes to a normal wooden boat. (01:41:50)
Continuity mistake: In the dream/memory where young Bruce is falling into the cave, the red book is in his right hand as he starts to fall. It is dark and raining. The next shot shows him at the top of the hole falling and he has dropped the red book. It is also bright outside with no signs of rain. The next shot shows him with the red book in his left hand. When he stands the book is in front of him, too far away if he held it. (01:30:00)
Continuity mistake: When Bruce slides across the table, both pumpkins go the right near Dr. Chase. In the next shot, they are on each side of the table. (01:32:55)
Continuity mistake: When Edward Nygma is in his apartment after killing Stickley, we see him pasting letters for the next riddle involving the match head. However, when Bruce and Chase are in her office looking at the riddle after it was delivered, you can see the letters are in different positions than the earlier shot.
Continuity mistake: Bruce's hair is much flatter and messier in the garage than in the previous scene outside when Dick is leaving, even though the garage scene happens directly after.
Other mistake: When Batman puts the lit torch to the cable and the cable breaks; the vault goes back into exactly the same place where the helicopter lifted it out from; connected via a grapple that Batman put through the wall. Ignoring the logistics of how this would be possible, it tightens the grapple, which surely, with the weight of the vault, would have ripped itself away from the wall.