Can't Clear all of Fog on the Map, Stuck at 99%

You'll find that you can't clear all of the map because of your clan buildings and potentially clan members. 

You can fix this by either

1. Using a map item from your inventory which should reveal the last section(s) 
2. Leave the clan and reveal the last few sections you were missing (though not advised)

Though it doesn't particularly matter, as during the Chronicals, the map will get 100% revealed for you anyway, so it's probably worth just waiting till that chapter has passed to get 100% revealed map.