A mother rabbit may eat her babies because something has frightened her or because she is skittish and confused. She may also be suffering from a dietary deficiency.
If a new mother rabbit is stressed or fearful, she may respond by eating the litter. Instinct may be telling her that the likelihood of her litter surviving would be better in another time or place.
Given an unstressed birth, eating a whole litter is rare, but eating one or two kits is not uncommon. The mother may have discovered that one of the kits is injured, defective or too runty to survive. In rare cases, a doe may habitually eat her newborns, possibly because she suffers from some nutritional deficiency. In such cases, it is best not to continue breeding the animal.
After giving birth, a mother rabbit normally licks her newborn kits clean. Then she eats the placenta and all of the other materials that came out with the litter. This behavior is common among small mammals because placental material provides nutrients that the mother needs after giving birth and may stimulate lactation. Eating the afterbirth may also be a way of removing traces of childbirth, which might attract predators.