Axe Cop normally determines if someone is good or evil by their kicking style. The one time he inadvertently killed someone good, it was a mermaid.
When bad guys do high front kicks, their heels are more prominent. Good guys don't cover their faces with high front kicks.
Axe Cop wishing that Flute Cop becomes a ghost would normally be a Fridge Horror (as pointed out already). However, if you know the fact that spirits who aren't really dead (like nymphs, for example) exists in the world of mythology (and even some modern day fiction like Ben 10), let's just say that Flute Cop is still a living being despite being in a form of a ghost.
In Episode 22, Axe Cop wishes that Flute Cop could become a ghost. Axe Cop killed his own brother. Fortunately, he gets better.
While probably not intended due to the fact that Malachai is very young, Telescope Gun Cop poisoned the candy canes that the Smartist family ate... Meaning that he may very well have been planning on murdering the young Axey and Flutey, but only failed due to luck on their part. In the TV episode "Birthday Month", this was indeed Bad Santa's plan. Axey survived because he hated the rainbow cherry flavor and fed his candy canes to the dog. Yet, in "Taxi Cop", we learn that Axey and Flutey grew up together as brothers but had their minds wiped of the experience.