Yes it's because some anemones or corals are too strong for some clowns... That being said it's wont hurt them as long as they go away within a month or two, but if it persists longer it may leave the clown suseptiable to infections. But it takes alot to get to that point. As long as their not white looking spots your ok. If it's white spots it could be ick, but thats just one possiablity if their white.
I would just keep an eye out an make sure the black doesn't turn into red...
Re-evaluate what is in your aquarium and if the condition doesn't improve in a few weeks, remove the culprit or remove the fish from this exposure.
Just so you know they call it Hyper Melaninization cause by contact of a coral or anemone that has stung the fish and causes pigment discoloration...
Good luck!