My brother pulled up a bass this May that had what looked like bruises on it like you described. It was caught in the state channel east of Zachs Bay. I had read a story over the winter that said some Chesapeake fish had lesions from Phiesteria. This is the toxic algae that has caused brown tides down south. We never did find out for sure what it was but it looked nasty and bloody. Didn't want to touch it.