I read a couple things. One, it might be an enemy squirrel trying to re-use the nest for its own purpose, so it gets rid of the babies. The worse idea is sometimes the mom (in mental issue or not) will think one of the babies can't survive on its own, there is something wrong with it, and rather than have another squirrel eat it - it will. Sometimes the mom will think there is something wrong with the whole set of babies and will eat them all. Strange.