Check your magnesium levels. Sometimes Croceas and certain color maximas will get BROWN spots around the mantle "loops" if the magnesium level is to low. It is also caused by light part of the time. If you throw a clam in a tank where it is getting to much light, it MIGHT develope spots on the same place on the mantle until it has has a chance to adjust to the light. Is it trying to tilt to one side? If it is light shock, they usually try to lay on their side a little bit to cut the excess light off from getting to their mantle.
If you try to do a freshwater dip to an already healthy clam that does not have a pathogen or bacterial infection, it will most likely stress it out a LOT. Freshwater dips I usually only use a, the clam would go one way or another' sort of thing.
EDIT: If you are talking about any other color then brown, like white spots, then that's a completely different thing. A pic would really help though.