I've noticed this sort of thing too.
I've previously assumed it was because of the mesh size jump and the general quality of the mesh around the edge of the control surface -- but maybe there is something there that can be fixed.
I'll mention it to Dave.
Unfortunately, even if the control surfaces are not deflected, they still get 'cut' into the mesh. This is good if you're calculating control surface derivatives, but a hassle if you just want clean non-deflected results.
We have the option to turn off control surfaces (in terms of communicating them to VSPAERO), but we don't use that information to avoid intersecting them.
When I added cutouts (for windows) to the visibility analysis, I needed to be able to selectively intersect subsurfaces. I could probably use that code to do that here too...
In the immediate term, you could copy/paste the wing, delete the SubSurfaces from the copy, and then use two Sets -- one with control surfaces and one without -- so you can quickly switch between analysis modes.
Rob