Just monitor him closely. If he scratches often, more than a couple of scratches every few minutes, then it might not bode well. You can look into gill flukes, ich, etc.
But only once in a long while, I wouldn't worry about it too much. My chocolate mimic tang does this once in a while and has clear skin, eyes, and his gills flaps normally. So if it's not to bad of scratching, I would just monitor closely.
HTH
