I've had the items in Breezehome in Winterrun scattered around upstairs and down when entering.
My bookshelf which was full of books had books scattered on the floor and a basket was stuck in their place, a basket which was never there by default.
It seems like the saved xyz cords is being transformed in someway to cause this.

At times when I've loaded inside of the house the wall on the loft does not load.
The housecarl Lydia stays in one place in the chair, tries to get up turns around and sits down again in the chair, she never does anything like use her own room or her own bed.
Makes her sort of worthless as an npc in the house.

Something similiar is happened to me. When I first bought the house, I also bought all the upgrades. So then I went to the house, looked around, put stuff on walls, etc. then realized it was 4 in the morning, saved inside my house, and went to sleep in real life. When I loaded the game the next morning, all the tables, bookshelves, and other items like that had dissapeared, along with all the walls that should have been on the inside of the building. All of the stuff that was on the said objects, were now on the floor. I fixed this by going outside, then back in, but all the stuff is still on the ground.

There are a few threads in this forum with the same problem, hopefully it get's patched as i really enjoyed pimping my homes in Fallout/Oblivion, easily lose a lot of hour's doing that .

I have the same problem with my Solitude home, reloading a save game fixes it for me.

Yeah reloading fixes the missing walls but nothing fixes the screwed up item arrangment.
It's also annoying that there's no way to place items in your home as in previous games.