General Breeding

How likely it is to create deformities greatly depends on how closely related the parents were. For example if the original mother and father were siblings, then a son of that mating also impregnates his own mother or sister the chances of defects in the resulting babies are much higher than if the original mother and father were not closely related. It also depends on the genetics of the individuals, for example if they had the roan gene then inbreeding greatly increases the risk of getting lethal white pups.

I assume the hypothetical situation we are talking about involves an incorrectly sexed pup being left with the opposite gendered family members, in which case much more concerning than the chance of defects is the risk of complication to the mother/sister. For the mother the risk of complications is greatly increases due to it being so close to when she last birthed and the fact she would still be lactating when being impregnated again. For the sister the risk of complications is also high as she would be getting pregnant at such a young age and would still be developing herself while pregnant.

Inbreeding certainly can create deformities, and is more likely to do so in some cases than in others. But it doesn't always happen.

I had that situation with my first guinea pigs years ago. I had gotten a female from a pet store and she was pregnant. I suspect the father was her brother. She had a single male pup. My mom refused to get another cage so I left them together. It was about 4 months before the Mom got pregnant again. That time she had three girls and a stillborn boy. They were all healthy and by that time the male was separated so no more babies. Apparently there was something underlying wrong with them because only one of them made it past three years old. The vet said it was probably a genetic heart defect because of the inbreeding.

@pigmommy89 I had a similar heartbreaking run with a pregnant sow I picked up from the RSPCA a decade back now. She had three babies and none of them, including mummy pig, made it past 2-3 years of age due to a genetic flaw. It was devastating nursing them through it.