A couple things. I've had this happen to my anemonefish a couple times. I've had trouble catching them and sometimes just left them in the tank. About a week later... all better. No idea why.
I've also caught them before and put them in my hospital tank. Medicated, it cleared up, and they went back to the reef tank. So you can catch them and treat them. But you'd be surprised how often they simply get better on their own.
Adam