Firstly; why would you want to stop them?
They are rabbits, digging is a totally natural behaviour to them, you won't be able to 'stop' it.
You can provide them with an enriching environment, tunnels, boxes, hidey holes etc in their run.
Is their run attached to their hutch, or is it seperate?
Could you mesh under the grass/soil, relay it then have the run there, so they can dig safely?