If then seem to go on fine then let them live, but if they are in any pain it's better to give them rest.
sometimes the mother bites some of the tail of the pups when she gives birth bacause she tries to helt them out, but In your case I think the others are right, I would keep a real close eye on that line and don't breed with those pups, no matter how good workers they migt turn out to be its' not ok to breed on deformed ferrets!