Here is a link to nutritional requirements of lab mice:
http://www.afrma.org/bc_mineralproteinmice.htm
For breeding girls, 16 is a bit too low so there is a slight chance that she's eating the babies to gain what she's low on. However, this still takes something overriding instinct to protect/raise.
Mice can also be genetically predisposed to killing their own young. Mostly you see it in inbred strains but I've even seen it in genetically diverse strains. Culling is the easiest way to deal with it because even though she might start having 'normal' litters with no problem, her babies have a higher likelihood of continuing the pattern.
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