Black spot disease.
http://www.dnr.state.mn.us/fish_diseases/neascus.html Actually a bird parasite with snails, and fish as intermediate hosts. Does little harm to fish, and is self limiting in the absence of piscivorous birds, and snails. Mussel glochidium attach themselves to the gills of fish, and are not embedded in the skin.
Gulf Killifish is a good ID. Here is a mud minnow.
http://www.dnr.state.oh.us/dnap/rivfish/mudmin/tabid/1709/Default.aspx Similar, but not your fish. Mudminnows are actually more closely related to pike, than they are cyprinids.
