This is not related to worms, and with all that space in your run its not bullying. What brand and kind of feed are you fermenting? I'm thinking protein deficiency but it could also very well be live/mites. You said you saw no signs of lice or mites though, so it's probably not that.
Feathers have protein, so if your feeding a feed with a lower protein amount, (18%, 16%) then that may be the problem as they will eat each others feathers for extra protein. I would switch to a 20% protein feed and see if that helps if you aren't giving that much protein already.