Female cat doesn't recognize son?

Unlike humans, the bond between Mom and kittens (or puppies) is broken once weaning is done. They do not stay close to them and the babies then become just another cat up for competition for food, attention, etc. Have you had your cat checked by a vet? Cats will also do this is they sense something is wrong with another animal around them. It's worth checking into. But chances are, there's just something about him she's not keen on.