Just found out the hard way that I've been losing books in Hearthfire. Often times I will clear shelves to reorganize, and I belatedly realized that some books are simply disappearing out of existence. It's really bummed me out as I was having fun putting together this massive library of books. I have no idea how many I've lost, but for example I had a shelf of all the 2920 books that I owned plus Palla 1 and 2. When I clicked on "activate shelf", it only listed the two palla books. When I clicked off, all of the 2920 books disappeared and were gone.
Yikes. I waited until the GOTY edition to play Skyrim specifically to avoid stuff like this, and I'm tremendously disappointed that this has happened.
I also had the house reset all its items on the shelves (displacing most everything in my trophy room) and the odd mannequin bug, but those already seem to be documented.
One thing for the next Elder Scrolls game - please make item movement and shelf placement a lot more user friendly than it is right now!