Well without seeing the holes this is hard to figure out. It could be the "HLLE" or "HITH" problems. (Head and Lateral Line Errosion, or Hole in the Head) These are relatively common problems that typically occur with water quality problems or problems with the fishes diet lacking in certain vitamins or minerals. Easy solutions for those are to work extra water changes into your maintenance schedule. (I usually recommend every week doing 20-25% changes for most fish. If they eat mostly live food you may need to increase the amount of water to 40-50%. For a few small fish in a bigger tank then usually every other week of 25-35% is good) The diet problem is a more likely cause especially if you feed your fish one type of food predominantly. You may want to look for vitamin fortified foods as well as some different brands and types of food including frozen, live, and fortified foods and rotate them so you are not feeding one kind of food all the time. One other possible cause has gone around on the internet as a possible cause of this. Generally it is discounted as "voodoo medicine" but those who believe this say if you put a titanium grounding rod in your tank this eliminated "stray voltages" that cause irritation to the fish. Since these grounding rods are cheap I just throw one in anyway.