I'm currently working on the Dungeon Master quest (loot three dungeons on each planet).

On Vulcanus, I have looted one dungeon so far (quest progress is 1/3). Another one is fully destroyed, but not yet looted. This happened at least one mod update ago.
When claiming the second dungeon, it isn't counted towards the quest completion (progress stays at 1/3).

I wouldn't mind going out and looting a fourth dungeon, but I'd like to keep the map size down.

Thanks for the report. I'll look into this.

I wasn't able to reproduce this following the steps you described. I'll consider it as having been indirectly fixed by a recent update.

Understandable. When loading the save again, neither of the two yet-unclaimed dungeons would advance the quest when being looted.

Haven't played in a few days. Will try again when I get back to it. Thanks for trying to fix it.

Ok, I think I figured the actual behaviour out. The initial quest completion shows 1/3, because one dungeon had to be looted to unlock that quest.
Looting one more dungeon seemingly doesn't do anything, because the counter gets updated to 1/3. Looting another one, pushes the counter to 2/3.

The previous message had me loot a single dungeon, check the quest progress directly afterwards and give up, thinking the quest isn't updating.

btw, the new quest "too useful hex cores" initially shows 0/500 progress, despite me being at 700ish when loading the save. It properly updates on looting the dungeons (I guess any expansion does that), but it would be nice if the progress is shown.