If this is her first time, she might not know what to do. Sometimes does just do that. If she continues to kill any of her other litters, then you may want to consider getting rid of her. Sometimes some rabbits just aren't good mothers. I had a hen that would start killing her chicks when they started coming out of the shells, so I'm not going to let her set anymore. Just sometimes animals do things like killing their young.
I would take the babies out and try to hand raise them. She may do this if this is the first time she is a mother and doesnt know what to do