They are not harmful. This could be what you are seeing:
"BLACKSPOT FISH PARASITE My son has two spring-fed ponds with bluegills and bass. When we fillet the fish, some have dark spots in the meat. I remember reading about it in one of your magazines and cannot find the article to determine if the fish are okay to eat. If so, what are the dark spots and does it only happen in spring-fed ponds? Also can we stock trout with the bass and bluegills?
Glen Bawek Arcadia
Fish Health Specialist Sue Marcquenski responded to a similar letter in October 2004 regarding black spots in perch. Here is her updated response: The black spots you see in the muscle of the bass and bluegill are larval stages of a parasite, cleverly called “blackspot.” The adult parasite lives in a fish-eating bird such as a kingfisher or gull. Parasite eggs are shed in the bird’s feces and when they contact water, the eggs hatch and the first larval stage emerges and infects snails. These larvae mature and in time are shed from the snail into the water. The larvae have tails and swim until they find a fish host, and then burrow into the skin or muscle of the fish. Here, they develop into a third larval stage and black cyst walls are produced, covering the larvae.
The black spots we see in the meat are actually the black parasite cysts. When a bird eats the infected fish, the larvae mature into adult parasites and the cycle begins again. Thoroughly cooking the fish will kill the parasites, and in any case, they cannot infect people; they can only develop in birds.
Almost all fish are susceptible to the blackspot parasite, so if you stock your pond with trout, it is very likely that they will become infected too. In the past 10 years or so, the number of fish-eating birds has greatly increased in the Upper Midwest, and snail populations have survived well over our mild winters. The blackspot parasite has taken advantage of this situation and will maintain its life cycle as long as the birds, snails and fish remain abundant in a lake or pond."