Digging litter out of the litter box is a hugely annoying problem. My rabbit, Graysie, did this for most of her young life, and I tried all sorts of unsuccessful methods (huge covered litter boxes, different types of litter, clapping, yelling, etc. etc.). Finally, this surprisingly simple solution ended my frustrations: I purchased metal mesh/chicken wire and metal snips from a local hardware store, cut the chicken wire in the shape of the litter box, and after pouring in the fresh litter, I placed the tight-fitting metal wiring on top. The urine and droppings fell right through the wire and Graysie wasn't able to dig the litter out. Success!
Feel free to leave comments about how you solved one of your stubborn bunny's naughty habits!