Hi Ioannis,
Could be Lymphocytis. My Percs had it and I treated them with Maracyn 2. I think the best thing to do is ensure good water quality. It supposedly cures itself if the conditions are right.
I'm not sure if that is what you are seeing, but since you said white cotton puffs and it was on more than one fish it sounds very similar to what I had.
DO a search on Lymphocytis and see what you think.
Good luck!!