My 2-month chihuahua puppy has tiny bald spots on his head. There is no soreness or itching and he seems to be very healthy. The vet did not know what it was. What could it be?

I am not sure what it is. You might have another vet look at it.

Are there scabs present? Any redness? Did the vet do a skin scraping or use a Wood's lamp? I cannot imagine a vet saying they don't know what it is-switch to someone who wants to find out! Things off the top of my head: bacterial overgrowth (localized skin infection), yeast infection and on the way outside-demadex (Mites).