My condolences on your kittens. A similar thing happened with one of my cats once, and it taught me a hard lesson about having pets. She had more kittens (9) than she had nipples (8), so I knew immediately that at least one wouldn’t get fed. I tried to rotate them out, but that only worked until one of the mama cat’s nipples was bitten off, at which point she wanted nothing more to do with them. Understandably, in my opinion. Result: despite my best efforts with kitten formula, heating pads, etc, all nine kittens died. It was like a little kitten Jonestown, really horrible, and I felt so bad that I couldn’t save them. So mother cats do abandon their kittens. If this is her first litter, she may not have known properly what to do, or how to take care of three rambunctious youngsters. Some cats just do not make good mothers, no matter how much practice they have, and should be discouraged* from having future litters.
Fleas also can contribute to kitten deaths (any small animal deaths, really) by consuming/ allowing to leak out too much of the total blood volume, which is very tiny already. Should you find yourself with kittens again*, you should ask your vet for flea control measures for mom and her environment before they’re born, and for baby-safe flea control once they’re out.
That said, my recommendation is to have your cat spayed. Many vets will do it for very cheap, not more than $65 or so, and sometimes for cost if you have a hardship or catch a special deal. For cheap vets, check your humane society or animal control agency for a listing.
To me, kitten death from natural causes isn’t something to be sad about. Things happen, and if you were providing a caring, loving environment for them, which it sounds like you were, then there’s no problem. It’s nature’s way. What is sad to me is irresponsible kitten production that leads to overpopulation, with no available homes, and abandonment in shelters, on highways, where ever it’s convenient to dump them. The best abandoned kittens can hope for is euthenasia, which is sad, considering how preventable kittens are. Preventing unwanted kittens (and any kitten that does not have a home already lined up should be considered unwanted) does a service to cats everywhere. It’s part of responsible pet ownership.