There two fish, the dottyback and firefish, while generally good fish by themselves are not good to put together.
Dottybacks tend to be very aggressive, and firefish about as docile a fish you can get. Putting them together usually causes exactly what you have seen. The dottyback beats up the firefish.
Sometimes you do get lucky and they will adjust to each other, but I'd say one is going to have to go. Of course, if you have another tank, this could be easy. Otherwise, return one to your LFS, or sell, trade, or give away one of the fish.