Eating 2 babies is completely normal. There is nothing wrong if she raises the rest of the litter. She may have known there was something wrong with the 2 babies, they may have been still born, there may have been too many babies for her to take care of properly, etc.

The mother's diet, or water needs may have also not been properly met.

2 babies is no big deal out of a litter that size. I would keep her around.