Nature is certainly weird, its possible the kits would have been stillborn (with mum having an infection etc) I have heard of absorption before.
Its like when a mother animal rejects one of her brood, they usually look fine to us, if only a little weak. Nature only deals with the fit and strong. There is no time to care for weaklings at the expense of the whole litter.
Its harsh, but it is very effective at keeping a healthy herd, pack (or for felines) solitary hunter. She will be much better able to have a litter when she is in peak condition herself.
;)