Apart from a couple of CTDs early on and a couple of quest items stuck in my inventory I havent really had any problems in my 180 hours of playtime.

But I think things are about to change.

I am starting to get invisible people and creatures, was attacked by an invisible bear, a couple of quest givers have been invisible when I returned and an invisible theif tried to rob me.
There was a big section of the water texture missing outside Solitude, I could swim in it and diving gave the usual effect of being under water but it was clear from above no matter where you looked at it from.
Leaving the cell and returning fixes the problem but I cant help but worry that I might be heading for something more serious.

My charcter is at level 42 and my save file is 14mb.

It's random, my unpatched game had the same water problem the 1st time I was up north-west from Winterhold, and it was with my 1st character at around level 10. Haven't seen it with any other character ever since. Just to let you know, I agree that it should be looked into and fixed, but I think you shouldn't worry too much.