Continuity mistake: During the bank scene, the Joker shoots the bus driver and he falls dead in front of the bus. As the Joker approaches the Bank manager to put the gas can in his mouth, you can still see the body. But after he removes his mask and walks toward the bus, the driver's body is gone.
Continuity mistake: During the opening bank robbery scene, the Joker reaches down to toss a duffel bag of money to the school bus driver. He is holding his pistol in his left hand and reaches for the bag with his right. But in the very next shot, his pistol is in his right hand and the bag is in his left.
Continuity mistake: In one of the first scenes with Det. Ramirez, you see her holding a cup of coffee. She switches between holding the cup with two hands, then one hand and finally two hands again. The cuts in the scene are immediate and linear, so she could not have changed how she holds the cup in between cuts.
Continuity mistake: Just after Gordon gets a call from Batman saying, "Gordon, I have the Joker's location, Pruitt building" it cuts to an aerial shot of the building. On the building there is a construction banner with the logo DAVIS, with a blue anchor shape logo. Then later on, when Gordon has the binoculars and says, "Why would they choose a spot with such good weakness" there is another aerial shot where the building banner now read BOVIS, with a blue arch logo.
Visible crew/equipment: When the Joker gets on the bus, after blowing up the hospital, about halfway along inside the bus is a large camera set-up. It can't belong to Mike Engel's news crew as it is not only too large to be hand held or shoulder mounted (it is one of the IMAX cameras used to film a shot from within the bus that wasn't used in the final cut) but also has a thick black cloth draped over it for the cameraman to work beneath. Obviously not a camera used by any news crew.
Continuity mistake: When Batman is removing the part of the wall with the bullet in it, we see the bullet hole is off-center, to the left side of the block that Batman carves out. In the next scene where we see the mounted gun shooting specialized bullets into blocks, Bruce compares the block he removed from the apartment, which is in a plastic bag, to the holes left in the sample blocks. The hole in the block from the apartment is now in the center of the block, not on the left side as it was when he removed it.
Continuity mistake: During the scene where Alfred tends to Bruce's bite wounds, the angle cuts several times between Alfred and Bruce. When the camera is on Alfred, Bruce is mostly looking down towards the wound. When the camera is on Bruce, he looks straight at the camera.
Continuity mistake: As Batman appears in the bank vault, Ramirez looks to Gordon. The scene cuts to Gordon, who acknowledges her to leave the vault. When the scene cuts back again she is already a few meters behind Batman. There's not enough time for her to cover the distance.
Continuity mistake: On lower 5th, the SWAT driver yells lock and load. When he does he has 2 cable ties in loops on his left hand side of his jacket that are exactly equal in size, both the loop and the "tail." We see outside the van for a few seconds. When the camera returns to the driver, the loops are now different sizes as evident by one having a longer "tail".