I don't breed rats but I do breed mice and dwarf hamsters. I can only tell you my experience and hope it might help you. The only reason my mice have eaten babies in the past was if they were stillborn, or I accidently touched them while cleaning the cage. I've also read that stress and the presence of the keeper can cause this, or even others in the colony. Was the first one alive or dead when she ate it? Are you sure the mother ate it, if not take out all the other rats in the cage and wait and see if she eats the nex one! Hope it works out.