My alsatian had puppies with its son is this why its puppies are dying?

What did the vet say when you took them in after being born? Have you called the vet after the first one died?

There could be many reasons.

Newborn pups can be very fragile, and without proper care can often have problems.
Chilling is a common cause of death for young pups. Do you have the room at a constant temperate? Do you have a heat lamp or pad?

How old are the puppies?

Are they feeding? If they are older than a few days how much weight have they each gained?

Has the mother been stimulating them to urinate and defecate?

I will echo mogranns post and ask what the vet has said? They should have had a checkup within 24 hours of whelping, both mother and pups.

Inbred puppies don't die because of that, unless of course they are REALLY inbred.

They could be dying for a number of reasons. Parasites would be a big thing to have checked out. Production of mother's milk would be the second thing to check out...

Please know that just because an animal has babies, doesn't make them a good mother. She could be laying on them, being too rough with them or not laying long enough to feed them. They could have been born prematurely and aren't fully developed inside. Tons of reasons puppies die. If you want to find out for certain, please make an appointment at the vet to have them check out. They should be checked by a vet anyway to make sure that mom and pups are healthy.