Rodents usually eat their offspring as a result of several things(and it is kinda common). If the mother gets nervous or feels threatened they may eat their children as a way of protecting themselves. Also, If food and water supplies are too low the mother may reduce the size of her litter by eating some of the offspring so that the food and water supplies will be adequate. To reduce the chances of this happening, do not disturb the babies until aleast a week has passed and keep more water and food available than usual.

Hope that helps a bit. I would not worry to much sometimes these things happen.