Usually with the mice, I leave them alone for about 4-5 days after they have their babies, and then I clean the cage. And even then, I pick up the whole pile of babies, nest and all, and put it in a container. Then I put the mothers in a separate cage so she doesn't stress over the babies.

If you can, cover her cage and put it in a dark, quiet place. Make sure she has food and water and leave her alone for quite awhile(a few days). If this is her first litter, I wouldn't worry about it. Sometimes they can stress out and it happens.. If it happens a second time though, I usually feed those females off. It seems to be a genetic component as well.. I know I've raised up some mice from a small litter, have them breed, and they tended to eat their children too.

Hope this helps!