Could have been a raccoon or an opossum. Also, tomcats will kill kittens they have not fathered, usually by biting the neck....could have been the kitten was killed and then something else just took advantage of the free dead meat.

I know that I'm beating a dead horse here, and that the kittens are not directly in your care, but this why it's not safe to leave them outside. The life expectancy just isn't in their favour.