In my experience, if you do a decent amount of hard braking, you tend to develop squeeks well before the brakes are worn. I would assume it has something to the with some mild glazing of the rotors or something. I'm not quite sure what your squeaking is like, but I have some very mild and light squeeks that pop up once in a while. Most times it wont even do it again when I'm listening.
Normally brake pads are NOT covered by warranty, since you can destroy them in a pretty short amount of time.