Sorry to hear that.... mother rabbits will often actually eat their young babies if they get in the slightest big stressed.
It was also her first time so maybe she was too inexperienced.
Next time leave them all alone for about a week.. only put in food and water away from the nest and don't spend any time looking at the babies or making any noise around the area.
After a few days the danger period is reduced.. and once they get the fur they are fine to handle. Once they start exploring away from the nest you can pick them up... but its always a good idea to not let the mother see you doing it.. and make sure your hands smell like the rabbit hutch by rubbing your hands in the bedding.
Better luck next time!