I've noticed that the attack natives button is bugged for some uncolonized provinces. When, pressed it simply takes your military power without actually starting combat between your army and natives. I'm running no mods so I've no idea what could cause it. East Timor is can example of a province where you don't seem to be able to attack natives, somebody try it out to verify it's not only me experiencing this issue.
Cheers
Cheers