Ok so I don't know how to answer this from a snake owner perspective (I have never owned or bred mice), but I am a mammalogist and can answer it from a rodent behavior perspective. There could be several reasons.
Many animals will engage in this behavior if they feel that there are not enough resources to care for the young, such as not enough food or a high-stress environment.
Another reason: males have been known to kill/consume offspring in an attempt to bring females back into breeding availability faster. This varies by species, some rodents have fathers that will help with child rearing and others have males that are uninvolved and therefore might participate in this behavior.
A third reason: defective litter. If an offspring comes out with an abnormality mother's have been documented killing the young, and even the entire associated litter. This is something that can occur more readily with inbreeding due to inbreeding depression.
A fourth reason: young mother. Some mothers abandon/kill their first (or first few) litters if they feel that they are "not ready" to be mothers. This would be very unlikely in a small rodent though.
But, with little rodents it's most commonly stress related, and that's my best guess. So something is stressing out your mice. It could really be anything. Too bright/dark. Too hot/cold. Too loud, too small of cages, too little exercise, too many mice together, the male is too pushy/aggressive. Something stressful bordering the cage (like a watchful cat or something). Really could be tons of stuff.
Anyway, there's my two cents!
