In the edited version when the Joker punches Batman and he falls off of the giant boxes in the flashback, 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 disappear a split second later.
When the Joker starts the "Our Family Memories" home video, 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.
When Batman calls Ace on the Joker, the satellite system is damaged. It shows the Jolly Jack warehouse and the beam on the same map. The beam is heading at a very steady rate and would have arrived long before the end of the fight.
In the edited version, Tim throws the gun away in the flashback after the Joker wants him to kill Batman. Yet, after the Joker electrocutes himself, Tim falls to his knees and the gun is visible by his side.
In the uncut version the Joker slashes Batman across the chest with a knife to break free of his hold, later on when Joker holds him up so Tim can shoot him the slash mark across the bat symbol and the blood on his chest is missing.
The Joker's appearance in the movie is based on his original Batman:TAS design. This contradicts a previous cameo in the Batman Beyond TV series where a wanted poster of The Joker is seen featuring a mugshot based on his "New Batman Adventures" design.
After the scene with the holographic Tim Drake and the automated weapons, Batman gets in the bat-mobile and runs a search for jolly jack, which arrives at an abandoned candy factory. There is no mention of where Terry heard of jolly jack.