I have a similar issue with a region I can't figure out how to get to (Helcus Stronghold of Lightning)(HSL), unless I missed something. I haven't searched all of the underground areas for secret tunnels (I don't know if they can exist anywhere else but the main map). None of the secret tunnels on the main map go there, though. Even though the HSL waypoint shows up on the map, clicking on it goes to a nearby waypoint instead.
I have also experienced that before - where clicking on one waypoint takes you to a different one in the vicinity