Pretty easy to check to see if he's been fixed. Feel. If you can feel "marbles" (seeing as he's a small dog. I would have said prunes for a bigger dog
) inside the sac then he was not fixed. If you can't feel anything inside the sac then yes, he was fixed and is acting on instinct.
If your girl is in heat then it would be a normal thing for him to do.
How old is he? At what age was he neutered? Was he used for stud before being neutered? That would all have a bearing on how he may react to a female.
Meanwhile - keep them separated until you know for sure.
This is something that should have been talked about before bringing him home when you have a female who has not been spayed yet. Then you could have taken the appropriate measures to ensure this did not happen.
IF by chance he is not neutered I would hope you would do the responsible thing and not allow your puppy to have a litter. She would be much too small and young. Please abort for her sake.