It's made of materials that slowly decompose into the ground!
...maybe. :0
Maybe the trainer has jedi powers @_@
Don't worry. The places where Legendary Pokémons reside in are barely visited, so no one would notice. ;PBut seriously, it must be messy after you've caught a legendary and left about 80 Pokeballs on the ground
I think it just disappears into your pockets, or something along the lines of disappearing.