There are several reasons
Poor nutrition, having food is not all that is required having food that meets their need is.
Stress (very common with mice)
Lactation issues, the babies will either die or be culled by the mother.
Babies died mother clean up (that's what they do they clean their dead)
Bad females.
I can take time to build a good colony and cannibalism can be avoided but you may need to start from scratch with a new group if their is no good explanation.
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