Why do baby bunnies poop a lot?

Rabbits use their feces to mark their territory. If your rabbit is pooping all over, that means he's feeling territorial, defensive, anxious, etc. If you want to reduce this behaviour, consider spaying/neutering your bunny, and consider what you can do to your bunny's habitat and lifestyle that would limit his stress.

When they aren't marking territory, rabbits like to use a certain spot in their habitat to go to the washroom. This could be a corner of their cage or, if they're given one, a box or private area of some kind - especially if there's hay there. If you want to improve your bunny's bathroom habits, consider litter-training him: this way, your bunny will only use that one box to urinate it and (for the most part) defecate in, and won't use other furniture or areas in the cage.

See the related questions below for more info and helpful links.