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.

Audio problem: When Tim enters Gordon's office, you hear Tim greeting Barbara, but it is Barbara's mouth that is moving. When Barbara replies, her mouth isn't moving.

Continuity: When Bruce plays the clip of the Joker appearing at the rooftop party, the audio clip that plays with it is not the same as when the Joker actually said it during the attack. The clip seems a bit more subdued than the actual voice track.