The bigger the litter, the higher probability that something can go wrong and you'll lose a bunny. Oftentimes the loss is early when your bunny has a "peanut" kit. You know to expect the loss, and do what you can to help keep the baby comfortable until it passes.
Unfortunately, there are times when an older kit dies. Recently we lost a 4 week old due to anorexia. We noticed that half the litter was starting to wean, but half was still relying on mom to nurse. The weaning babies all had nice fat bellies, but the nursing ones were starting to feel like rag dolls.
We started to place the nursing bunnies in a box filled with hay during the day to encourage nibbling. While most figured out that the hay was to eat, there was still one female that refused to nibble more than a few minutes each day. Eventually the baby passed because it just refused to wean, and mom's milk wasn't enough for her growing body to sustain her.
It's difficult to lose a kit at this age because you've invested so much time into ensuring they are healthy and well socialized. Young babies you can feed milk, but if a kit refuses to try eating solid foods there is nothing you can do to force them.
You find solace in the knowledge that you did everything you could to provide the best environment and foods necessary for your bunnies. Seeing the remaining kits thrive and move on to their furever homes is heartwarming. Yet you always remember the few that don't make it.
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