Rats and mice are actually highly prone to dystocia/difficult labors. So as mentioned by Sorril, one getting stuck in the canal could have caused this for sure.
I actually just had to separate a first time breeder female out for what I thought was just a low birth rate at first, but when I checked back in with her the next day, she had eaten all her babies. The female that had been housed with her dropped 16 healthy babies, so *shrug*. She'll be culled from the breeding group because I don't want the possibility of that trait continuing.
Sometimes we really don't have a reason why they end up as they do.
For the best production for breeding, you ideally want to shuffle the male between groups of females. For the moms, give them a week or two to recover after taking away the weaned litter. The faster she gets back into breeding, the more likely she'll be to have a lower production or issues with the pregnancy.
I cycle one male in a 5 tier rack. Every two weeks he gets shuffled to a new row. That gives my girls a little time to fatten back up a bit before they get bred again.
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