Your kitty might have ear mites as well, kittens seem to be really prone to them. Check her ears and see if they seem to have a waxy buildup and see if she seems reluctant to have you poke around by them (of course, she might just be skittish in general when you play with her ears). I had a kitten with ear mites once and she scratched a lot around her neck and ears. It's a super quick fix though, just take her to the vet and they'll douse her with some medicine and she'll be feeling better immediately.