Generally it's a good idea to keep prego moms by themselves. Females will tend to fight over the babies , usually by having a tug-o-war with them. This could be the cause of their death. Although sometimes some females just aren't good moms and will eat the babies for no apparent reason.
I produce about 2000 rats a month and sometimes it happens. I would say I have about 1 in a 100 kill their babies.
Don't sweat it and just keep at it.
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