It doesn't matter if you keep mice together or not (and all mine breed quite well in 1.2 trios)...if the parent isn't a good one or the mice sense danger (which is far too easy for them to do), they will eat the babies. They also do it if the litter isn't healthy or if they're missing protein and calcium in their diet.
The best thing to do is make sure the tubs they're in are opaque or covered somehow, kept in a low-traffic spot so they don't think they're exposed to danger. Give them a good food mix (Becky's Mix here on the forum is great!) with senior dog kibble for protein. And watch them for the next cycle (once they get pregnant the first time, it doesn't take as long the next times). If they still eat the babies, then there's something wrong with the breeders and you should probably start again fresh.
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