Deliberate mistake: You might be wondering where Terry suddenly comes up with Jolly Jack all of the sudden after escaping the lab. In the commentary, they say that the Joker, in his transmission to Terry in the lab, was supposed to be eating out of a candy jar with "Jolly Jack" on it, but couldn't have it due to time constraints.
Deliberate mistake: The device that rises out of the Jolly Jack factory and summons the laser beam shatters the decorative head, appearing to do so for the first time. However, we have already seen the destructive beam in action, meaning that device must already have emerged. This was acknowledged on the commentary by the filmmakers who wanted to show the visual metaphor of the Joker driving the young Tim Drake insane.