I have been doing dungeons repeatedly while waiting for the bug to get fixed. I clear a dungeon and when I leave it shows the checkmark that it was cleared but as soon as I log out it removes it and acts like I never did it. Sometimes it doesn’t show that I’ve cleared it without logging out. I tested it both ways doing 4 dungeons in the upper scosglen/dry steppes regions 4 different times and every round I did, the checkmarks vanished.
This is not a bug. The checkmark only indicates that you cleared the dungeon for that game instance.