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.
Answer: Because he stole a chemical from his lab.
But Batman knew that with it, Clayface could permanently retain his shape and Clayface desperately wanted to be Matt Hagen again. In a sense, Batman stopped Clayface from becoming human.