I've seen this happen several times and have housed kittens that had been rejected. There are several reasons for this:
Illness
According to the feline advisory bureau this is when she rejects them because she thinks they won't survive anyhow. These congenital birth defects include deformities of the limbs, spine and other body parts. You need to consult a vet if the animal has these problems.
Mom Problems
The mother might not have proper nutrition herself and will reject any excess babies because she can't properly care for her babies, plus a mother cat can only nurse eight kittens at a time any excess will be rejected. If you neglect the mother and show her little attention she may also reject the kittens. Showing a new mother how to nurse her kittens by laying her on her side and guiding the kittens to nipples will also prevent rejection.
It is VERY IMPORTANT that a kitten receive the colostrum from the mother. If the kitten is rejected contact local shelters and rescue groups to find a surrogate mother so the kitten may receive the colostrum. In the event of rejection you will have to also hand feed the kitten a substitute for the mother's milk which you can likely ask about at the nearest vet. I may have added problems you may never have to deal(Hopefully) with but I just wanted to make sure you know various reasons for rejection so you can be prepared.
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