Is the flaking common, does it hurt your motor?

I can't remember what the material is but no it doesn't do any harm.

I thought it was teflon or something like that?

Yeah its teflon. Supposedly not a big deal to come off, probably just helps the rotors last longer. Maybe helps with heat. Wearing off might affect the boost pressure negatively, since the rotors wouldn't be as tight if much of the teflon is gone.

People injecting nitrous or alcohol tend to lose the coating fast.