Think of your pet bar as just shortcuts to your spellbook. It doesn't really matter if an ability is on the bar or not. It can be cast or autocast directly from the spellbook, and unfortunately all new abilities start with autocast defaulted on. This is something we might be able to fix, but in the meantime, peek at your pet's spellbook whenever it gains a level to make sure nothing has changed. Cower can surprise you, because it/si something a lot of players passed on before -- understandably, because even if effective it's not a very fun thing to spend points on, which is why we just give it away now.