No one is concerned why Cindy is holding the janitor's head after finding out that he's used her dog as an ingredient for "Biscut Balls".
That's not abnormal for this universe. Heck, considering what he's like, they might have been happy that she did it.
She has the chances
If you try to steal from Buggs's cubby when Ms. Applegate isn't high on the pills, she'll tell you to stay away from the cubby, even if it literally has a knife. She would normally send you to the principal's office if you showed it during Show and Tell. Considering Ms. Applegate really wants to get rid of Buggs, it's unknown why she hasn't ratted him out for having a knife at school.
The Evidence
When Lily requests you get evidence something evil is going on, one of the potential items is a shoe belonging to Billy, a missing student. The other is a severed finger, however the only kidnapped or missing person is Billy, who has all his fingers when you find him. Even by the end of the route, it is never revealed who's finger it is.
Usually lightning has this reaction
Considering the talisman execution method is deadly lightning from the sky, why did nobody think to run back inside once it started happening?
De-mutation
So on the Principal's computer, red blends, green demutates, yellow switches the selection, and blue releases tank contents. So how exactly did the Principal mutate the creatures originally if there's no button to do that?
Perhaps whatever liquid was in the tanks naturally mutates things exposed to it?
