I cannot currently complete either the Thieves Guild or the Dark Brotherhood because of bugs in the AI system. Let me explain.

My current Thieves Guild mission is "The Pursuit". My objective is to meet Karliah in The Ragged Flagon but she is not there, she is currently stuck in the cellar in Winterhold.

This is also having an impact on my Dark Brotherhood progress. I am on the quest named "Where You Hang You Enemy's Head" where I have to employ the services of Delvin Mallory, a Thieves Guild member, however because they all think I'm a traitor due to not having completed "The Pursuit", I cannot talk to him. Instead, he says something along the lines of "leave me alone until this is all figured out".

This is really frustrating as I was enjoying these two Guilds and I've completed pretty much all other "main" side quests and the main quest.

Seems like NPC behavior is causing a lot of issues in Skyrim.

I wouldn't be surprised if this was not another symptom of problems like I reported about Skjor (couldn't find him anywhere to get the Proving Honor quest and the map arrows were completely out of whack) and many others i've been hearing about related to quests not being completed after you actually... complete them! Seems like the NPCs get stuck even after you complete the quests and the quest end is never "recognized" by the system.

In my case, in another quest error related to that, I just hit the NPC with a shield bash (any hit will do, actually) and the quest completed right there on the spot. I had to run to avoid a fight after that though

What's perhaps even more... serious is that in my case I had around 3 saves prior to the issue and the issue repeated itself even after I tried loading my oldest save. That tells me the world inconsistency that caused the problem was really old. I wonder if Bethesda can even fix these bugs. Might stop them from happening again, but fixing the ones that already happened? I'm not sure.

I really hope they can fix them as I really don't want to have to create a new character just to play those missions.

I will make a new character at some point but I just feel I'm not finished with my current one yet

For me Karliah and Brynjolf never show up at a later quest for the main thieves guild quests.