The holes are very likely scars or unhealed wounds. If the cat has always had them, then you shouldn't worry, it probably got them as a kitten and they didn't heal properly. If they are recent, maybe it's best to visit a vet.
Depending on the hole it could have been a boil. They start off as a knott and if not treated they get bigger. Then they burst and cause a good size hole and if that does not get treated, it could become a very bad infection and they could die from it. Please have it treated.
The holes could have been caused by injuries suffered in a cat fight. Perhaps, your cat is scatching his head with his nails causing the holes. If this is the case, try trimming your cat's nails. Insect bites may also be the cause.
Your cat could have gotten in a fight with another cat, a dog, or other animal. If the injuries apear minor and are not bleeding, lket the cat care for itself. If they are serious, take your cat to the vet for care.
