Visible crew/equipment: When the museum closes early and Joker calls to each of his cohorts, their individual chalk T-marks are visible on the floor where they all stand. (00:12:40)
Visible crew/equipment: When both Batman and Robin realise that even though the museum can't be broken into, it doesn't mean someone couldn't break "out" of the museum, as they rush to the museum's front doors we can see a chalk T-mark on the ground in front of the doors. (00:13:25)
Visible crew/equipment: At the end, Joker announces the unmasking of Batman and Robin, then when Joker turns and walks toward them, multiple chalk T-marks are visible on the floor where the dynamic duo are being held. (00:23:55)
Answer: There wasn't one singular city used. It was shot in and around various locations in California, plus on a lot of sets and backlots. Ex. Some scenes were shot in LA, some in Pasadena, some in Santa Barbara, etc.
TedStixon