
So much depends on what actually happened and why -which may be impossible to find out. The most common cause for pups to die would be inertia which would explain why they were alive and well on the scan. Was the bitch overdue for her breed?
I have two stories. The first my first Papillon bitch. First time she was scanned and two live pups seen. The evening before she gave birth I could clearly feel one pup moving about -no question about it. The next day she gave birth to one dead pup that had been dead for a while -it was entirely black and decomposing. (I'd ask your vet about the numbers and roughly how long they had been dead.) The second pup was also dead, so clearly had only just died. We decided to give it one more try so the bitch was mated again. This time we did several scans. The scanner said there were two pups. The vet who palpated said there were two pups. Again I could feel them move the night before. She then gave birth to two dead puppies; recently dead. Then out of the blue arrived one LIVE pup. He's now 5 years old and of course we kept him. He had no problem being a single pup, although he is the cockiest little git ever -here is a Papillon that thinks nothing of starting a fight with a dog many times his own size. The bitch was spayed.
The second story is about a Malinois, not my bitch but one I bred. She was scanned as having about 4 pups. I'd told the owner that he should expect pups early, from day 58 onwards, and certainly no later than day 64 at MOST. Any later and things would not be right as I know my lines give birth early. He kept going back to the vet who kept saying all was fine, kept scanning and showing heartbeats. Eventually the vet agreed to do a c-section day 68 (!!), again after having scanned in the evening of day 67 and seen live pups. All the pups were born dead. It was just left far too late. The vet agreed it was their fault and wrote off the bill plus some for future treatment.
The bitch was mated again and had 4 pups after a normal length pregnancy (I think it was 62 days), all were born alive although one died after a few days. Certainly small litter for the breed but this second time no problems at all with giving birth. Pretty sure the bitch had inertia the first time and the pups would have lived had the vet agreed to do a section sooner.