Waypoint / 100% area completion bug
I had this bug as well. Sometimes it helps to enter the actual areas, (which is a pain in the keester, I know) Sometimes when you go to one of the places that has a known “new” waypoint (Ashford and Brisban have new ones related to Guilds) it will update the other maps.
I have this problem too. I have done the 100% but it keep saying me i still missing one point.
In the last few months they added four new waypoints. One in each of the following; Cursed Shore (south end of map in Mausollus Sea)
Straits of Devastation (just off the shore of Elysium Beach)
Plains of Ashford (southwest corner just below Decimus Waypoint)
Brisban Wildlands (northwest corner just below Gallowfields Waypoint)
NOTE: The Guild Wars 2 Wiki does not show these new waypoints.
These wp also do not show up on your map until you visit the area that it is in