She could be rejecting an "imperfect" kitten, or she could be moving them. Cats normally like to have their kittens in a quiet, darker area. If you've got kids (esp young ones), the kittens must be hands-off. Don't let strangers (to the cat) go in to look at the kits.
Sometimes mother cats will sense when a kitten isn't right. Sometimes it's a real problem, like an intestinal defect, etc, and nothing you do is going to help. Other times, there is something wrong, but something that the kitten can live with.
The vet advice is excellent. And get the cat spayed, too. There are already millions of unwanted cats out there.