Your puppy probably has a congenital deformity and was born this way. If the other toes on the affected foot are normal, than your dog should be fully functional.
Another cause for missing digits occurs when an inexperienced mother over-grooms her off-spring and accidentally chews off the digits. This is uncommon, but sadly can occur.
I think you should give your vet another chance. Any vet would be surprised to find missing digits. It is still out side of the norm.
take to your vet , but sounds like he was born that way . does he walk ok on that foot. if so he probley born that way and that makes him a very neat puppy.