I HAVE heard of situations where puppies are not visible on an ultrasound when there is a smaller litter (such as 4) at 30 days. However given the fact that they are now born....I should think that the breeder should offer you a pup from that original litter that you had thought didn't take.
What raises HUGE
flags for me is the fact that her so called "stud fee return puppy" is a puppy that has an overbite? What the heck type of breeder would take a pet qual puppy back from an outside breeding? Typically the stud dog owner would get a show pick male or female whatever had been agreed to prior to the breeding. And I would think that in event that the entire litter had disqualifying faults then the stud dog owner should take the stud fee money in lieu of a puppy.
I would get my money back and keep searching!!
Heather Peters