Angel fish with spots in side, what's wrong?

[Squeekers83]

This fish had some swim bladder issues and is not in the big tank because the other fish were picking on it pretty bad. It's been swimming noraml for quite awhile but I kept it seperate to try and let its fins heal up some more and now its getting these two spots on its side. Somedays they look grey but then there are other days where they look a nasty black. I know somethings not right, just sure what it is. I don't quite know how to treat it or what to treat it with. Any suggestions would help. Thanks!