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.

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.