Millions of bunnies do this :lol:
As long as the litter tray is changed 1 or 2 times a day it shouldn't really be a problem, rabbits are quite good at keeping themselves clean.
Perhaps provide something softer that he will like lying on instead?
If you don't already you could put a small layer of hay on top of the litter, so most of the wee will seep down to the actual litter and wont come in contact with their skin