Crud, I was hoping to add a couple of S boats tied up to the tender.
Anyway opening as a normal mission I get this kind of thing;
Obviously the bases don't actually need waypoints since this ain't an earthquake simulator so they shouldn't be going anywhere, but the rest of these errors are with stuff that I didn't put in, those units were from the stock game AFAIK. I checked those three and all are set as docked, so what's with the "too close" errors?