I’ve seen a few posts for older versions of Blender tackling this same issue. Often their solution is to change the Normal in Velocity to 0 but for me, that just affects the scale of the rocks. All the rocks have their origin right in the middle of their mass.
So I feel like it’s down to the position of the particles in the modifier list. I put the particle system from the top to the bottom… but now they’re under the surface 
Anyone? … anyone?
You’re not exactly showing what you’re doing so we have to guess. But if you scatter the particles on a terrain mesh and then displace that mesh this is what will happen I guess.