I’ve noticed that when you are using the map, it automatically switches to your current ‘layer’ in the zone you are in, but it also sets the maps in the other zones to be in the same layer too.
for example, the Gilded Hollow guild hall map is underneath Tarir, so uses the underground map layer. but if you want to warp to maps in Tyria, such as Lions Arch, all of the waypoints are on the Surface layer, so waypointing requires you to change the layer before you can select the waypoint.
it would be quite useful to have the zones display the waypoints faded, like it does in the map when you are above or below a waypoint in the same zone as you. that way you can still warp to the Traders Forum (for example) without having to change layers