Apologies in advance for WoT / TL;DR. It's written that way so the bug can be recreated by QA more easily. Spoilers ahead obviously:


There is a quest line that involves clearing the place out and re-activating its ancient defences - you progress via journals discovered on dead researchers. The quest is obtained from the notes of an Imperial Captain near the entrance to the Dwemer city proper, after you kill the giant spider Nimhe. (Killing her is a pre-quest given to you by the NPC Calcero, as she has been stopping progress in the main part of the cave/tunnel excavation).

If you don't collect the journals in order, the quest log doesn't award you for picking them up/having them in your inventory.
I like to explore a whole area, and find alternative routes and clear places out before progressing. Especially in big labarythian areas like Dwemer ruins, which are laid out to be explored however you see fit, so I can imagine several players have encountered this. The first researchers journal that you're supposed to get is definitely the easiest to reach, in the Sleeping/Living Quarters.

But I went on and explored the rest of the main area - and went through the armoury first - where the NPC with the 'second' journal is - and through the upper level door to the armoury, back into the main area - the bridge connected to this upper door is where the 'third' journal and NPC is.
I had these in my inventory, as I figured they would be part of the quest. I almost went up into what was obviously the 'final' area, the Control room.

Seeing as this was just a singular route, I opted to go back and 'start' the 2nd phase of the quest, so that I had 'cleared out' all prior areas, and do what I had been sent here to do. So I backtracked to the Living Quarters.



The quest updated off the journal from the NPC in the living/sleeping quarters and told me to collect the 3 journals of the other researchers. 2 of which were in my bag already.
It didn't award me as having them already, and created duplicates instead of all the journals/notes for this quest that I currently had so far.

Fortunately the other 2 journals I had picked up 'ahead of time' were optional it seemed, although it didn't say (optional) in brackets in the quest menu.

I got the last one on the way to the control room, and it gave me the next phase of the quest. But even after that, the diamonds next to 'find this NPCs journal' for the 2 that bugged still didn't fill in - (I was hoping progressing the questline would make the quest correct itself, as it looked like they were a mandatory component at the time).



I had tried to fix it by dropping the 2 journals - (although there were dupes in my menu, when dropping them only one of each book appeared) - and picking them up again after I had recieved the update from the body in the sleeping quarters, as they had the little 'quest item' arrow overhead whilst lying ont he floor. I also tried putting them back on the relevant bodies and 'finding' them in the correct order now I had the new phase of the quest, but to no avail.

Thankfully I could still complete it, but was a bit peeved at having my immersion spoiled by not exploring this open space in the games 'correct order'. Moreover, if I had collected the journal from the last NPC on the way to the control room, I suspect it would have made the quest unfinishable.

It seemed odd, seeing as how I've been pleasantly surprised when I have had quest items before recieving a general Misc quest - handed it in straight away - and gotten specific different dialogue because 'I had already done it', which I thought was really cool.


Hope this helps, and also prevents others falling into the same trap.