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The problems occur with running the dungeons set to "Mythical".

The problems :

#1 : Two ( creatures / things ) will not spawn ...
.... a lich named Bevelros, in the Iron Outpost.
.... S.U.Z.I.E, in Junktown.

#2 : The "Skull of Caldeus" is never found in Deadwatch.

#3 : The "Scroll for the Blademaster" && "Caldeus Heart" are stuck in inventory.

#4 : Two or more "Artificer’s Revolver Components" in inventory, if you repeat fishing in that particular slot.

#5 : The Rusty Red Blade && other specific blades ( Sutton, etc. ) never have their "upgrade scroll" found.

Couldn't find any way to file a bug report at "Airship Syndicate".
Just to add...

Actually, I have encountered a few of those problems in regular mode.
- never found Bevelros (though I did not repeatedly check the iron outpost, I did redo Deadwatch several times and found his tomb, and a secret room with a chest and an empty box)
- extra artifact revolver parts
- never found any upgrade scrolls

Conversely, I have had things work correctly in NG+ mode.
- found S.U.Z.I.E.
- found skill of Caldeus