Hi frizzby,
The stones turning green, I guess is due to Algae growth which is a very primative form of plant life and is a natural process, which is more than likely due to the shade of the tree.
Every Boy-scout knows that moss and algae always grows on the north side of the tree, pretty good advice to avoid going round in circles if your lost in the woods!
If the stones are pebbles, you could try moving them around with a rake occaisionally,hence the old proverb 'A rolling stone gathers no moss' or 'grass dont grow on busy streets' If larger boulders, an occaisional scrub with a stiff brush/broom might do the trick, but any chemicals could harm the tree roots. Good Luck Tbird+