well there is a good chance the male killed and ate the babies as they weren't his... i would have put her into a tub alone personally esp since mice can get pregnant immediately after giving birth... no time for recoup!

mom could have also eaten the pups as she would have been pretty stressed out with a new male in the tank with her... she also could have been a first time mom and the added stress of moving her could have caused this.

feed her well... lots of yummy healthy treats (thin peanut butter between two stone wheat thin crackers... for example) and see how she does with the next litter. female mice REALLY like another mama mouse with them when they have babies... to help out with the litter. just so you know