Continuity mistake: When Clay-Face makes things like crab claws they're red. Yet later on when he fights Batman again in the TV station they're light brown.
Continuity mistake: The clay used to bind Germs goes from a creamy light brown to dark brown.
Continuity mistake: Clayface has clay in the shape of the right hand on his chest when fighting Batman. A few seconds later it's suddenly in the shape of the left hand.
Answer: She escaped off-screen and created a copy of herself to fool everyone.