If you haven't done all the strongholds, there are a few in those.
Other than that, just run around the map to all the blurry bits and you'll find them. Or look up a map online.
I would assume it is a Stronghold one OP is missing.
The easiest way to figure out which ones you are missing would be to use one of the interactive maps where you can check off the ones you already have. (I can link the map I've used, but don't want to unless you want it.) As far as I know the only waypoints that are locked by quests are the ones attached to strongholds.
Just to correct the post a bit: there's no need to do any sidequest to unlock all waypoints.
https://d4builds.gg/map/, enable waypoints from the filters, compare to your own in-game map. If you run to a missing waypoint and it shows as locked, you'll need to clear the nearby stronghold to open it. There's a total of 6 waypoints which are placed inside stronghold areas.
Filter for waypoints and check them off to find the ones you’re missing.
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