Ok it could be a number of things, for the best advice we need a little more info. can you give your water test results for
ammonia
nitrites
nitrates
ph
(Post the actual reading please. dont state Ok or fine.)
some more info on your setup,tank size, fish stocked, fish size.
without these we have little to go on. also a pic of the hole would help. as for what it may be, as a guess it could be HITH,(from poor water) a sensory pit(natural) or just a small wound. there is a post in "emergency" with some pictures of fish related problems it may be of help it you try to identify the hole from this too.