She will not have a safe OR healthy pregnancy. She is far too small. Yes, she IS stunted. Or it is possible she is a slow grower. If she has a high worm and/or coccidia load (they are different things), is genetically small, or has not taken in enough nutients to support proper growth, it can result in stunting.
She was just bred, yes? So you need to get to your vet promptly for a medication called Lutalyse. Follow the veterinarian's instructions precisely. The medication will terminate her pregnancy.
Unless you can bring her up to at least 40lbs (the bare minimum weight a pygmy should be before becoming pregnant), then consider her a pet and do not breed her again.
