It's not they best idea for a pup to eat bees. Sooner or later one is going to sting. My vet told me to give my dog Benadryl after he was stung by a hornet. The dosage was one milligram per pound of body weight, but I started out with half that dosage and it worked just fine. I think there is a liquid formula Benadryl now for babies that would make it easier to set the dosage for a dog smaller than 25 pounds, since 25 mg is the smallest Benadryl capsule size I'm aware of.
I have no idea how to make your dog stop catching bees. I never could get Bear to stop until he got stung.