Shredder and Ra's al Ghul viciously assassinating every Arkham guard they find. Did we mention this is a Nickelodeon movie? They evidently did spare some of them, or at least didn't bother killing the ones not in their immediate path.
When Batman becomes a mutant bat. Special mention that he's heavily implied to maul Mr Freeze to death. He even throws Two-Face out a window (while he likely survived due to being mutated it shows he was clearly trying to kill them).
The mutated Arkham inmates. Joker and Two-Face stand out, with Joker becoming an albino cobra and Two-Face's head splitting into two separate cat faces.
Harley manages to be quite unsettling to look at despite only mutating into a hyena, mainly due to her crazed red and green eyes and her massive fangedSlasher Smile. Her mutation is likely one of the nastiest as well, what with her jaw bulging with oversized, carnivorous teeth before it finally expands and lengthens (along with the rest of her mouth) into a canine-like muzzle to fit them.
Hell, Scarecrow was disturbing before he got mutated!
The fear hallucination Leonardo sees under the effects of Scarecrow's gas. He turns to see his brothers, and the crow-mutate Scarecrow looms behind them and spreads his wings. A murder of crows swarm the three and devour them, flying away to reveal their desiccated, eyeless corpses on the ground. And as Leo falls to his knees and takes one of their hands, they blow away into dust.
alone is horrifying. It almost reaches Cronenberg-levels of Body Horror.