Continuity mistake: Trying to protect Salvo, Riley punches two thugs. The second one is a red bearded man. The big boss urges then the other baddies to attack, and redbeard is way behind him, hasn't leaped into action yet. (00:11:35)
Continuity mistake: The chain gang trio is having a bit of chit-chat underground. The social worker Batman came looking for hauls a giant rock on top of the cart, but the rock is gone when the gallery starts to collapse. (00:08:25)
Continuity mistake: The fat boss tells his underling that the prisoners will bring him "twice the gold ore." He asks then "Do you hear me?" The fan is in front of him or behind the back. (00:06:15)
Audio problem: Alfred brings breakfast. He says "Rise and shine", but no mouth animation is included. (00:07:10)
Plot hole: Alfred manages to find the bad guys because not only they grabbed the supposedly homeless guy off the street (Bruce in disguise), but also somehow brought his car to the scrapyard. If they knew it was his, they would have known something was off (a hobo with a car?) and they would have not got rid of it after more than a day. If they didn't, and they just towed out a random car, Alfred had extraordinary luck - nothing in fact would lead to believe that the truck was even related to the car.
Other mistake: Bruce remembers who he is, which somehow gives him also the strength to bend metal (!) and escape. A new prisoner is carried in the camp by the guards, but...he's not new at all. He was already there the first day, standing in the group of prisoners that was eating. And the guy who escorts him is the same that less than a second later spots Bruce from the watchtower and blows the whistle. (00:06:20 - 00:14:30)
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.