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It sounds as if she had the litter before you separated them and hid them well. Males start to pester the females to mate a few days before a litter is born and he has likely mated with her even when the first were delivered. With a litter that size she will still have looked quite large which you have mistaken for still pregnant.
She will need some extra help or else the newborns will struggle to survive. Take out the male pups from first litter and put them with dad. Keep them warm and supplement feeding with plenty protein and generous food.