On my hunter I found that if Cower is not on your petbar (ie it's just in the spellbook), it keeps getting turned on to autocast at random. So I always keep cower on my petbar, even though I never ever use it. Hunter abilities that can have autocast turned on, seem to have a tendency to get it turned on at random when they're not on your petbar. So if your pets have prowl and you're sick of prowl getting auto-turned on, you'll have to drag that out to your petbar too.

It sucks that blizz can't fix this, but it ends up that most of your petbar ends up being occupied by abilities you DO NOT want the pet to use, just to keep it from becoming autocast.