Here are the glitches and problems I have discovered.
*For players of Skyrim, beware of what you read for the quests, it does contain spoilers.*
Quest glitches:
Pantea's Flute- Talked to Pantea after finding her flute through her showing me on the map, I've seen that some people find it prior to speaking with her and experience the same problem, I "give" her the flute back, the quest is registered as completed. Alas, the flute is still in my inventory and there is no way to be rid of it.
Ill Met By Moonlight- I fast traveled to Falkreath after speaking to Hircine, the ring causes me to change into a Werewolf, the entire town dislikes Werewolves and pursuits me. I get to the jail, only to find him inside of the cell, but transformed. I leave because the town followed me into the tiny jail room. I run away far enough to wait and transform into a human again and find Sinding idly pacing in front of the Barracks in Werewolf form! No one seems to notice. I attempted to kill him but it doesn't register as completing the objective for the quest, therefore a quest I cannot finish.
Odd Problems:
In my home in Solitude there are 2 weapon racks with 5 slots, I can only place weapons in the three middle slots. The two on each end cannot be used.
Companions seem to "lose" you at random times. I'm not shimmying up mountains, they just lose me in a dungeon then I have to wait a number of hours until my companion returns to the designated home after tiring of waiting for me. They also do not follow very well either. Another problem with them is they seem to be reluctant to engage with enemies fighting me right in front of them. Their weapon is drawn but no desire to fight.
Not a problem, just my own mistake, it would be nice if I could do some sort of quest or task to allow me to reset my perks or at least take away perks I do not wan't and gain the perk points back to be appointed to useful skills I actually use. I'm sure this wont happen, but I admit it is my fault for being indecisive and using perks while unsure what the bloody hell I want done with them. I had to dabble a little bit.

Books in the book shelves have odd spacing sometimes with gaps in between. It would be nice if they would stay upright instead of flop over, it is understandable in terms of the physics but I can stand a few books upright in a larger space than is needed. They are also all hardcover...
While dual wielding weapons, the one in the right hand is sheathed as normal, the one in the left magically disappears.
Talking to companions and asking them to wait or do something is a bit iffy also. The pulsing icon showing where they will go or what to do will be there after giving them a command, on top of the fact that they have a hard time completing the command. After attempting the command the pulsating icon will be present if you strike up conversation with the companion again causing you to tap 'A' a few times in order to get to the conversation options.
Many of these are just petty complaints, but the small things really add up to the immersion.