They are not actually pooping in the food bowl, but rather right next to it. The food bowl is only maybe two to three inches across, so they really can't poop in it. It seems more that they are eating and pooping at the same time - you see them eat and then when they move there are fresh poops...
We have rescued two bunnies and are in the process of litter box training them. We have a 4' x 4' pen with a cat litter box being used as the litter box. (That's what the rescue organization used). In this litter box we have a dog wee pad on the bottom to absorb the pee, hay, and care fresh...