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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
Sorry for necroing this but all the things you've mentioned, OP, are RNG-based. Meaning that you may or may not encounter them at any difficulty. You have to re-do the dungeons until RNG lords are on your side or just forget about it and move to the next dungeon.
Post edited June 11, 2019 by BlueBangkok
Yes, it is pure RNG. I had to run Deadwatch like 7 times in first playthrough to get the skull, then got it immediately in the first room of second Deadwatch run on NG+.

Yes, it sucks that quest items are stuck behind RNG but the game is unfortunately made like that to make you replay the dungeons.