You might be onto something with the Compute Terrain's patch size. You could try with a much smaller patch size (the size of the stones, say) to verify that that's what is happening. If so, it's not a bug - just a limitation in the accuracy of the slope represented by the patch size.
Be careful when using a very small patch size, though, because the patch size needs to be large enough to prevent displacements from changing direction too rapidly. It's also needed for the surface layer's "intersect underlying" feature.
Matt