Rabbit pills can be easily swept up or vacuumed and can be directly applied to plants as fertilizer. The trick to getting the rabbit to minimize the number of pills left around is to respect their cage or boxes as theirs. Don't move their belongings or rearrange their stuff. When they are in their cage, leave them alone. Remember that they are leaving their droppings to help find their way to the proper place to go.
Some rabbits love to dig in and kick the litter out of the box.
To avoid this, you can get a covered box or experiment with different textured litters. Also, some rabbits back up so far in the box that the urine goes over the edge. A hooded box would work for this, too, or a tub with much higher sides. A number of issues could be at work. The rabbit may have a health problem such as a urinary tract infection.