There are myriad possible reasons. We need to know a lot more. What is your setup, how established is it, what are water readings, etc, how old is the fish?
I have 2 new Percula Clowns. Bought both at about 1". They both developed brown spots, one has mostly kicked them with growth, one still has spots and brownish tint to the top of its body. I did a search on reefcentral and found a lot of possibilities. I'm guessing mine were due to some weird growth stage and/or trying to host with something that gave them a reaction (I don't have anemones in my tank). The one with the brown still is smaller, and I am trying to target feed.
But it can also be something more serious requiring treatment. Like I said, we'd need to see a lot more about your setup, as much info as you have.