The poo you descibe is cecal pellets, rabbits make two types of poop. The dry round pellets you usually see it the litter tray and the soft, dark bunch of grapes type. This second type you don't usually see because they are eaten by the bunny as they are produced. They contain lots of important nutrients.
Hay is the most important part of a rabbits diet and pellets should be fed only in smaller quantities. How big a bowl are you feeding half of? I'd suggest splitting the feed into two, morning and evening and then they can't eat them all at once. Vegetables and grass needs to be introduced slowly, once they are adults and they have got used to eat they can eat a bowl full a day quite happily.
What time of day is she producing the cecal pellets?