When Deja Vu had her kittens, even though it was my 2nd time, I did extensive research (which I didn't have the chance to do 15 years ago, that one just came in from the street, ate, lay down, and had 7 kittens). This new cat looked so much like the one 15 years ago, that's why I named her Deja Vu.
Anyway, out of the 7, the next morning I found one dead. I rushed them all to the vet, hoping it wasn't something contagious. He checked them all and said they were fine, then felt the kitten I had lost and said it just didn't feel right inside. I wouldn't have known what to look or feel for. He said sometimes one is just not born right, and it's not anything anyone did or could have prevented.
When Deja Vu had her kittens (5 this time), there was one that was small, but I also began to notice after a few hours that she wasn't eating either.
I frantically got on the web, and based on everything I had read, and what I could do for makeshift in the house, I made a temporary KMR homemade mix (not recommended for more than a day, 2 at the most), and used the end of a very rounded chopstick which seemed the size and shape of the mom's nipples. I dipped that in the mixture, and tried very gently to get the kitten to suck on it. I stayed up all night trying and trying, at about 1/2 hour intervals. At one point suddenly she opened her mouth and made a really loud smacking sound, and the sucking instinct kicked in (it hadn't before). In fact, this was something I only found described on one site (there may be others, but I didn't find it). Luckily, it worked and she pulled through, but it could have easily gone the other way. But before you think you could have done something like that, read on....
I told you that story to tell you this one. When I was doing the research there was one thing just about every site said, and they all said it in almost exactly the same words.
And that was that sometimes, no matter what you do, no matter how hard you try, kittens sometimes die. It's a fact of life, and a downside of a very joyous experience. They can die within a day or two of being born, up to even 2 weeks later for absolutely no reason that we can see.
You shouldn't feel guilty. If the other kittens are prospering, growing and are healthy. then you are doing the right things. As someone already pointed out, there is little you can do if mother nature has not cooperated. Even humans have SIDS. It just happens, and the best way to handle it, in my opinion, is, as sad as you feel, put your attention on the kittens that are healthy and strong and surviving. That's what the mother cat does.