The most likely reason is they weren't getting fed. With so many babies, the mother rabbit will just hop into the nest, feed, and will not care about about the babies until the next feeding session. The stronger babies would have pushed the weaker babies aside. The babies tummies should look full after eating. If not, try grabbing the mother, and though it might make her unhappy, hold her and let the bunnies who don't look like they got as mush to eat suck. Make sure she still has milk though. I can not remember how much they should weigh at this age. I'm sure you could do your research and find out.
Hopefully someone else can help you a little more then I could. It's been a few years since I've had bunny babies.