According to
Bruce Timm, Tokyo Movie Shinsha, the studio that animated this episode, ignored the color instructions given to them and made their own color palette. The results were so successful, though, that Timm didn't mind. Per Timm: "I think when we shipped them 'Clayface,' they said to themselves: They think they know everything, but we'll show them how do do this show. We'll change Batman's colors. We'll do special color key treatments on the villains when they're walking over the green vat. We'll blow them away.' If that's their revenge, thank you for proving us wrong. I was so happy with that episode." "The sequence where Daggett and Germs are walking over that green vat, those characters look like they're three-dimensional. They look like they're rotoscoped. When Daggett slowly turns toward the camera, the shadows really wrap around his face. It's as if they're real! They did all those colors themselves. We couldn't even ask for those colors if we wanted to. They aren't even in our palette. They had to specially mix those colors."