I am sorry for your loss but things like that can happened to newborns
there are so many contributing factors that could have caused this from body
temperature, congenital defects, Hemolytic Disease

PLEASE contact your vet talk to him or her about what happened they can give
you more insight and more of a helping hand.  We can do what we can out
here, give you insight the best we can and a helping hand as best we can
but a Professional is required in this situation  They may need you to bring
the cat and kittens in they will know best.
Keep a very watchful eye of them.  Lets us know what the out comes is  and
if we can help in any ways possible

a very helpful site for you
http://www.maxshouse.com/kitten_care.htm#Newborn%20Kittens

Congratulations on the ovely Kittens, and im sorry to hear one died, how sad
and unfortunate. *big hugs*

In my limited experience, i could suggest it was the weakest one, the runt
as they say. It would be a good idea to take it to the vet for an autopsy, i
know that sounds mad bu if its bothering you and you have to know thats one
alternative. If thats not possible, as others have mentioned phone or talk
to the vet.

Rachael

Sorry to hear about the babe who didn't make it. How are the others
faring? If they're OK, perhaps it just wasn't meant to be for the
little one.

My sympathy on your loss and my hope the others are thriving.

Nature has it's way of weeding out the sickly and weak. Don't worry. Same
thing happened to my kitty when she had babies. It's natural
--
=^. .^=
Martha
http://marthalovescats.info
http://_martha.livejournal.com

I've seen this happen many, many times while working in a shelter.  It is not
that unusual, but needless to say, I am sorry for you to have to witness it
as it is quite sad.