Continuity mistake: Scarecrow's shoes are light brown in most of the episode. Yet once he's back in his cell they're suddenly dark grey.
Continuity mistake: When Batman stops the countdown it reads as 1:45. When Scarecrow starts it back up it's suddenly 0:14.
Continuity mistake: Scarecrow's pants turn red when he's on the catwalk turning on the pump machine.
Character mistake: The Scarecrow's thugs flee as his water pump machine explodes, yet he seems to have stuck around long enough to be affected by his own toxin.
Plot hole: It's never explained: 1. How or who helped Scarecrow escape from his cell or 2. Why he'd be sitting in there at the end in costume instead of prison garb.
Suggested correction: Something not being explained is not a plot hole. The manner in which Scarecrow escaped his cell isn't essential to the plot, and therefore doesn't require an explanation. And the reason he's left in the cell in his costume is for the same reason Batman was left wearing his outfit when he was imprisoned: because the doctor at the asylum felt removing his outfit in his hallucinatory state could cause him to become catatonic.
