Continuity mistake: Batman tears off the front of The Scarecrow's collar. Yet later in his hideout it's fine again.
Continuity mistake: Batman knocks the tommy gun off Anthony's hand. He is looking at the weapon that lies on the blimp, and then tries to seize it again. The weapon is positioned different between the two shots. (00:15:25)
Continuity mistake: Batman is analyzing Scarecrow's mask at the computer. During the whole scene the photo of his parents and the newspaper change position. (00:10:20)
Continuity mistake: Scarecrow just terrorized the security guard. His two goons approach him asking what did he do. The one with the grey coat has his Tommy gun in his right hand, the one with the brown coat keeps it off frame. In the second they are off camera, grey coat switched hands to the gun, and brown coat is holding his to his chest. (00:04:20)
Continuity mistake: Batman got rid of the two goons through non-lethal falls, and he is about to face Scarecrow. Scarecrow has his escape planned; he has his right hand on a lever by the armrest...or in the next shot, on a lever above him. (00:18:05)
Continuity mistake: Both Batman and Scarecrow's henchmen are reading the same newspaper, one with a "University Museum Benefit Tonight" headline. The same headline though has a different layout; the words "museum" and "benefit" have bigger spacing in Bruce's copy. (00:10:15)
Continuity mistake: Doctor Long pushes a button on the elevator's board. The key shines bright in close-up, it's not lit in the wider angle. (00:02:30)
Continuity mistake: Scarecrow's boots start out dark red then they're light brown later in the episode.
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.