If you had it for 3 months and are just seeing this now, I don't think it would be a parasite. You could try a Lugol's dip I suppose. Perhaps something picked at it after a feeding. I have seen crabs and fish eat the food right out of LPS after i have fed them and once the food was totally inside the coral. I had an arrow crab that would reach right inside the mouth and remove whatever it wanted. After the flesh is damaged, it's possible for it to fall victim to some sort of bacterial infection. ....Just thinking of possibilities.