Hello & Welcome to YT! I'm so sorry yr puppy is having this problem. I would call the Vet and inquire to make sure. Someone posted this article for me once when I had questions about using Ivermectin. Did the Vet do a skin scraping? If so, did it show up for Mites? I hope it gets better very soon. Also hoping someone can help that's had experience with this. Good Luck!
Demodex Skin Mites In A Dog and Human at ThePetCenter.com