Re: rats eating their young
What Deborah said.
It could more than likely have been cannibalism because the pup was already dead, it could have been insufficient protein to either sustain the mother or allow her to create milk, she could've just been a really bad mother, it could've even been that the other mother was "jealous" and ate the baby from the other rat (it happened to a friend of mine), it could really have been almost anything.
Re: rats eating their young
A young or first time mother will sometimes eat their young as well. Was this her\their first litter(s)? I've had young mothers do this and then become very productive with their future litters.