Losing newborns is not uncommon in mammal breeding, and I agree with the other posters - if it was a stray cat you know nothing about the history or health, even breeding health of the animal whether it be any sort of problems in the 'line' or bad moms. First litters seem to be somewhat of a learning experience, however cats are much more prepared instinctually and physically for completely unaided deliveries, unlike dogs.
Sorry for your loss, though. So hard to say what it could have been. I'm sure there are helpful cat breeders that could give you some insight if you can contact any.