I posted this same question a couple weeks ago. I got replies as it could be mal nutrition and to up the feeding dont think this is it. Black ich disease is what i will be treating now that i read ur post. Hope your succesful at getting it cured. I have two clowns they both got it at the same time. My tank had just got done with cycling when i added them. But ive been into reef tanks for a couple years now. Down graded from a 125g to a 30g nano. Gooood lucck hope they get better.
Young clowns are very easily stung by frogspawn hammer's and bubble corals "could be more but those are my experience" and the stings show up as black spots,
that's my guess
Mike

Hypermelanism, stings from corals?
Black ich is a parasite, I do not believe it just resolves. .