Why would a mother dog kill her puppy?

Question
My beagle, Daisy gave birth to her 1st litter of 9 puppies 4 days ago. One of the puppies was born with a cleft lip and palate, we took her to the vet 1st thing the morning after she was born. We decided that we would do everything possible to help this pup survive, between my vets advise and the instructions for dealing with cleft puppies on http://hennwood.tripod.com/cleft_pup_info.htm we have been bottle feeding her every 2 hours (even in the middle of the night) and although she lost a few ounces the first 48 hours she was finally back to her birthweight this morning. Last night at 6 when she ate she acted very hungry and gobbled down more food than she usually will and was very fussy afterward (it seemed as though she had a tummy ache from eating too much). Typically before/after her feedings I stimulate her to go potty and give her back to the mama, who has been treating her just like the other normal pups. However, last night when she was so fussy it was really making the mama upset so rather than leave her with her all night, we kept her with us in a basket with a heating pad for warmth and we returned her to mama as soon as she was back to normal early this morning.
Today the pup has not been wanting to eat like she normally does (her lungs have been sounding clear still and she hasn't been fussy) she would eat just not as much as usual. Then this afternoon we noticed the mama kept picking her up and holding her in her mouth for no apparent reason (pup was not crying or anything) and when the pup would squawk to be put down she'd keep holding her, eventually she would put her down (most times she would hold her for 3 minutes or so, but not too tightly). Anyhow we went to the store and were gone for about 45 minutes, when we got home we found the mama on the couch (not in her whelping box) holding the puppy by the head in her mouth, I could tell the pup was bloody and she her down as soon as she saw me. The pup was still soft, but not breathing, no pulse and it looks as though the mama bit her on the head. I am just wandering what could have caused her to do this (could it have been an accidental bite) I feel so guilty that I should have known, but other than picking her up allot there were no other abnormal behavior or aggression. She is acting perfectly normal with the other puppies (she never picks any of the other pups up) should I be worried that she will hurt them too, or was it because she knew something was wrong with that pup? Just to clarify, she was not "eating the pup" she was just holding her by the head and there was a cut where I'm guessing the mamas incisors were.

Answer
Hi. Unfortunately, since you didn't actually see it happen, we'll never know for sure if it was an accident or on purpose. She may had been worrying herself over the sickly puppy, and accidentally killed it (they do seem to know when something is wrong with one, even when we can't see it). She's a new mom, probably young, never had to deal with puppies before, and she may not have known what to do with the sickly puppy. On the other hand, she may have known something was wrong with the puppy, and was trying to get rid of it so she could concentrate on the healthy ones. We'll never know. Just keep a really good eye on her, and don't allow her to pick a puppy up anymore, just to be on the safe side. I'm sorry this happened.