Fog of war is a Pro feature. On a map with scale levels, a detailed hex normally takes its fog from the larger hex it sits in. Once it has fog of its own, it keeps that fog and ignores the larger hex. A detailed hex gets fog of its own when you paint fog on the detail level, use Reveal All or Hide All there, or when the party explores it with dynamic vision.
The sign is a patch on the detail level that doesn’t match the map above: a dark corner you hid for a surprise the party has long since found, or an explored trail that stays dim after you changed your mind about the area.
Fix a few hexes
Go to the detail level, open the Vision tool (V) and pick Follow parent in the fog brush. It only appears on a detail level. Paint over the stuck hexes, and each takes its fog from the larger hex again, and keeps following it.
Fix a whole area at once
Go up to the larger level and paint fog over the area with the fog brush. Any fog you paint there clears the fog of its own on every detailed hex underneath, on every finer level, and they follow the hex you painted from then on. This works with all four fog levels, so to keep the area as it is, paint it with the fog level it already has. Reveal All and Hide All on the larger level clear the fog beneath every hex they change in the same way.
The clearing only goes down, never up. Painting on the middle of three levels clears the finest level beneath it and leaves the base map alone. It also stays on the layer you painted, so the Underdark below the surface keeps its fog.
When not to do it
Painting fog on a larger hex also wipes the explored trail the party left on the detail levels beneath it. If you want to keep that trail, use Follow parent on just the hexes that are wrong.
Moving the party marker never clears fog of its own on a detail level; only fog you paint does. Your players see the change when the map next saves, shortly after you stop painting. See when your players get the change.