I would think that it could be from her teeth. She is still getting baby teeth and her gums could be bleeding some while trying to get them in. Mia was like that. My first and older one didn't have bad puppy breath but the younger one did (really stinky). After she got her adult teeth she didn't have bad breath anymore.
Anything you do in trying to train them as puppies most likely they will put up a little fuss. From brushing their hair and teeth to baths and so on. You just have to be consistent just like with children and show patience and lots of love.
Good luck with your new girl and enjoy her. All things will come with time.
Telea
