Atlas Passive (Uncharted Realm) Bug

The next patch (3.13.1c) is planned to make the /recheck_achievements command fix this case.

Or, you can allocate more passives when you unlock them, or you can respec then reallocate them, both methods will recalculate your challenge progress and fix it up.

If you didn't get any credit for a boss kill or Maven invitation, the most common reason is that you died and respawned, and the encountered was completed while you were in town. In which case you would need to try again.

Also it's worth noting that Maven Invitations do not share credit with party members, so if you ran a friend's invitation, you wouldn't get any credit for that.