There are several threads on Reef Central that describe large black spots on clownfish. It seems that this can be caused by a skin irritation from an zoanthids, anemone or possibly other corals as you suspected.
http://reefcentral.com/forums/showth...threadid=67167
http://www.reefcentral.com/forums/sh...hreadid=179513
http://reefcentral.com/forums/showth...threadid=42345