Weaning time is one of the most stressful periods in a young rabbits life. The rabbit is just transitioning off its mother’s milk to full dependency on a pellet ration. In addition the animal is being removed from a familiar surroundings to an isolated pen life.
Any help you can provide to alleviate this stress is going to improve the chances of the rabbit flourishing in the future. One suggestion is to remove the doe from the litter at about 8 weeks of age. The young should be almost fully transitioned to pellets and staying with the littermates helps the animal from stressing from isolation.
As you start to cull the litter, you might try leaving two or three of the littermates in together for a week or so to before starting to move them to individual pens. The entire process shouldn’t take more than two weeks, and hopefully eases the rabbit into a productive future.