After Batman defeats Ghoul, before he can move away he is immediately attacked by the Dee Dees, but the unconscious Ghoul is nowhere in sight after that.
In the edited version of the film, when the Joker punches Batman and he falls off of the giant boxes in the flashback sequence, for a brief second, a knife can be seen in the Joker's hand and a slash in the Bat-symbol on Batman's chest. Both of them disappear a split second later.
In the edited version of the film, Tim throws the gun away in the flashback sequence after the Joker tells him to kill Batman. However, after the Joker electrocutes himself and dies, Tim falls to his knees and the gun is visible by his side.
When Batman breaks through the projector window in the flashback sequence, he grabs the Joker and slaps him in the face. Blood can be seen dripping from the corner of his mouth, but it is gone in the next shot.
When the Joker starts the "Our Family Memories" home video in the flashback sequence, it shows him narrating it in the projector booth. There is a clearly visible microphone hanging down from the ceiling, but in the next shots showing him, it is gone.
In the flashback sequence, Harley Quinn's bazooka fires multiple shots without reloading and, at first, it fires a lump of rubber bands, then switches to cannon balls.
After the scene with the holographic Tim Drake and the automated weapons, Batman gets into the Batmobile and runs a search for Jolly Jack, which arrives at an abandoned candy factory. There is no mention of where or how Terry ever heard of Jolly Jack. However, Jolly Jack was written all over the Joker's getaway vehicle after he attacked Bruce at the Wayne Enterprises press conference.
Terry's jacket in the film is originally shown as brown. When Bruce fires him, it is purple. It goes back to brown again in the next scene. In the series most colors are changed while heroes are in Batcave.
When Tim enters Commissioner Barbara Gordon's office, you hear Tim greeting Barbara, but it is Barbara's mouth that is moving. When Barbara replies, her mouth is not moving.
At the end of the fight, Terry pulls the Joker's joy buzzer out of nowhere.