Was mom the only one in there with the pups? I breed rats and sometime this happens to me too. Usely its when I didnt get out there quick enough to get them fed, but have also had it happen a day or two after putting food out. I dont know the full reason of why they do that sometimes, but it does. Ive also gone out and have found my Male dead and have a hole in him from where the 3 females have eaten on him, couldnt figure that one out either.