They probably have bare butts because one or more of them are pulling out butt feathers. The offender probably still has theirs! I have only had very limited success at stopping this - but this post will bump you up and some of the more experienced BYC'ers should have plenty of great advice!
Too many roosters, not enough protein in their diet, a breed that doesn't do well with confinement, or too many chickens packed into an area. One or a combination of these are common reasons.