It doesn't look like this is a pot bunker issue. Ordinarily, your rough, the outward mesh, should bend down to the terrain and cover up the terrain underneath all meshes within - yet for some reason it does not do that in your images. You probably blame the pot bunkers because the bright fresnel glare of their pot walls sticks out like a sore thumb, yet if you watch closely, there seems to be a uniform strip of nothing along the entire mesh rough - and that is clearly not as it should be.
Perhaps you did some elevation work or strong smoothing of the terrain after you calculated the meshes - that would explain this sort of undermining. If I had but the first image without explanations to work with, my guess would be that you changed something on the terrain and did not re-calculate before building the course. But if so, you should be able to spot this in CF before noticing it in the game.
Another weird thing are those black lines beyond your rough spline. They do show up in game and are indicative of some weird Unity glitch or so that is described in older posts and that I do not know enough about.
I'm sure there must be a fix for this, I'm almost adamant that this is not a pot-bunker issue, yet have no other suggestions about this.
Also, the saturation of your rough seems off the chart, compared to all the other meshes. Inverness, eh?