Just in case it hasn't been mentioned yet...
*Quest name: N/A
*Type: Thieves Guild Misc.
*Description: Relatively early into the Thieves Guild quests you are given a full suit of thieves armor to wear; each piece adds to thief skills like pickpocketing, lock picking, etc. However, chances are decent that if you use heavy armor or are just doing the Thieves Guild for completion (i.e. not really focused on thief skills or thieving that much) you will have little use for this armor and will sell it. The most convenient place to sell it happens to be Tonilia, as she has a good amount of money and is (I think) the one who gives you the thief set in the first place. This presents a problem though, as you are later given a quest to upgrade your armor. If you sold all of your armor to Tonilia, your only dialogue option with her will inevitably end with her telling you to go find it. She won't go into her buy/sell screen and pickpocketing her for the armor comes up empty. I have not yet progressed much further so I don't know if this breaks any quests further down the line or whether it essentially makes her useless as a vendor/fence for the rest of the game as well as the short term. So far as I know, there isn't a replacement set you can get your hands on, though I have not tried killing any of the other thieves to check.
How To Replicate: Sell Tonilia all four pieces of your thief set and don't buy them back before she offers an upgrade for a piece of your set.
Stats: N/A
Other: N/A
Not sure if there's an official quest or not, but I'm stuck on becoming Thane of Riften.
The quest log says to check in with the Jarl, but there's no conversation options that will let me progress. She told me to purchase Sunnyside from her advisor and then check back with her. I bought and upgraded sunnyside in one go, went to take a look, but when I came back, speaking to the jarl would not advance me.
I ran into an identical problem as well. Not sure if this happens 100% of the time or just random chance or what.
On that note, I've noticed a glitch where with a bounty quest involving bandits, if you cleared that area before you got the quest, the quest doesn't auto update to complete or respawn the chief so you can complete the quest, making it impossible to complete so far as I can tell. This happened to me with a single tower so far and upon venturing back to the (cleared) tower, there were two bandits on the lower floor, but nobody upstairs and in any case no chieftain to be seen. Presumably this could happen for any bandit bounty quest. I am not sure if it would happen with the dragon bounties or not.
So, in the usual format...
*Quest name: N/A
*Type: Bandit Bounty Misc.
*Description: Apparently if you clear an area of bandits and then later receive a bounty to kill the chief bandit there, the quest neither auto completes (reflecting the area's cleared status) nor does a new chief bandit spawn there. It's possible that the bounty causes other bandits to spawn (not confirmed, may have just been random respawns due to time elapsed) but in any case the important one won't be there. Talking to the steward who you are supposed to turn the bounty in to presents no dialogue option to turn in the bounty. Have not confirmed whether this happens all the time or just sometimes due to a glitch in the code or what have you.
How To Replicate: Clear out a bandit area prior to receiving the bounty quest for that very area.
Stats: N/A
Other: N/A