After finishing the bloodstone pilgrimage in Almas Thirr I tried to get duties from Lloris Dalan who acknowledged that I had finished the pilgrimage but when asking about duties acted as if I hadn't finished it. It took me a minute to realize that I probably had to return the shoes to Herman Llothro which was indeed the case. The Journal doesn't mention anything like this so it may be wise to add/edit a entry about returning the shoes to make things a bit more obvious to prevent any confusion.
At the end of the quest called "Temple: The last will and testament of Ulmon Vathri" there is a bug that occurs when talking to the daughter Felani Iannus where she will turn hostile. Her wife, Marja Iannus will do the same when spoken to. This prevents the completion of the quest as you cannot select the needed dialog. The problem occurs towards the end of the quest when everything is taken care of and you have to speak to Felani at the dancing cup about the will of her father.
Nothing is owned in the Etana Egg Mine in Roth Roryn. Ownership should probably be assigned to everything except the Ancient Bowl, which is picked up as part of the quest Remnants of Resdayn.
Object named t_imp_setharbor_galleonin_decks lets you walk through it. exterior pillar of the ship unaffected. Unkown if other ships could be affected by this bug.
After completing the quest "Thieves Guild: Disarming the Tong" two tg members start selling their own jinksblades even though they recieved them for the purpose of selfe protection. Makes the quest feel a little pointless.
For the quest Trouble Brewing in Andothren, Nevusa Falen asks you to help her plant a spoiled potion on Hemmette Fauler to shut her business down for good. However, Hemmette Fauler's barter inventory already contains loads of spoiled potions. It's strange that I should have to plant a spoiled potion on her when there's plenty of evidence on her already. Perhaps having a high enough alchemy skill to recognize the side effects of the spoiled potions can allow you to point this out?