It's a bit strange the breeder did not notice that
I'd hope they will at least refund you the purchase price (or at least a percentage off)
I went to a seminar recently and there was a young Shepherd puppy (3 month old I think) there who was missing 3 back toes - his foot looked really strange all straight like as if you cut the fingers of your hand and just have the palm left.
He had other health issues as well but was a bright sparky happy pup
Definitely mention it to the vet, the pup needs a thorough check up but don't let it stress you too much
As long he's getting around define and not in pain it should hopefully not ever be a problem
(unless you bought him as a show dog)