I have been breeding rats for a decade I produce a few thousands each year and I have experimented various method, harem, rotating males, communal birthing, individual birthing etc

What tend to work best is to rotate males or females and remove the females when pregnant to let them birth in an individual tub, than once the babies are about 5 to 7 days move the females in communal nursing tubs.

This allows maximum production and minimum loss, while females are great mothers they are sometime to great and will fight over babies and when they are under 5 to 7 days their skin is very fragile, breaks easily and it lead to death.

There are a few possible scenario with your situation, male killing the pup, bad female killing her pups, lactation problem (pup died or were culled and than rats did what they do clean up) etc.