Unless you give them a job to do, like mining Gems or working out on the treadmill, your bunnies will wander around the burrow and amuse themselves. If you put a bunny somewhere and returned later to find it gone, look around your burrow and see if it might be hiding in a tunnel somewhere. Sometimes bunnies get inadvertently put away in your inventory, too. Try tapping the bunny icon on the RIGHT side of the screen to open your inventory, and you'll see right away if your stray bunny is hiding out in there. If it is, just touch its icon and drag it into your burrow.