Not exactly sure of the issue there but it is not uncommon to see things of that nature. The term "Freshwater" is really used loosely anymore, in my opinion, as most waters aren't really so fresh.
I have also seen things like this for instance alot while fishing for bullheads and other cats;
Neascus spp. (Black spot)-Digenetic trematode:
These parasites encysts within the skin of many species of freshwater fish. The fish in turn, surround the cyst with a black-pigmented tissue giving rise to black spots. These parasites do not usually cause mortality, but can be very unsightly. There are no reported cases of people becoming infected with these parasites by eating fish. There is no known direct control for these parasites. Indirect control has been attempted by controlling the snails that serve as intermediate hosts to the parasites.
Which is only one of the many things listed on this paper.
http://www.mass.gov/czm/wpfshlth.htm
So as to the exact problem with the fish you pictured, I am not sure..but chances are it won't be the first or last malformed or diseased fish you see, sadly