If the mother dog thinks there is something wrong with the puppies then she will eat then they could look healthy to you but they could of been really sick to her.
There are two reasons why she would do this:
1) It was a hidden illness that she could sense. Only a vet can say for sure if they WERE healthy or not. They are also capable of doing an autopsy for you for a fee.
2) she was inexperienced, especially if this was her first time. She may have had aggressive issues towards the litter. You should have taken them immediately away from her and sought medical help and professional advise from a vet. There is usually a number that vets have especially for emergencies.