The most common reasons are:
- Being disturbed especially in the first few days
- Improper nutrition or not enough food and water
- Lack of nesting material/hiding spots
- Overcrowding either with a very large litter or too many adults
- Taking back nutrients in a litter that was recognized as unhealthy by the mother (some will abandon and just stop feeding the litter in this case). Kind of an important note, but this doesn't mean that the litter necessarily was unhealthy, just that the mother recognized them as such.
- Genetics, in which case, they will continue to eat their young or abandoning them
It is not uncommon for mice to eat their first litter. This is especially true if females are bred too young.