When its on the outside I've read various explanations relating to water chemistry and it comes/goes with molts. Alkalinity and iron seem to be frequently blamed. However, the same thing can occur more internally and not in conjunction with molts. I went back and checked what I'd read on that and it looks like THE "black spot disease" I think I mentioned in another post isn't documented in cleaners like I thought it was, but I've read other hypotheses ranging from some sort of bruising/hemorrhaging to infection (which to me means nobody really has a handle on it yet).