I bought all the decorations, thinking I'll leave the 500 septim cost of cleaning for later.

But now I don't get the option from the stewart to clean up the house.

And it looks really bad since my alchemy and enchanting stuff is all mixed up with the skeleton parts and bloody stuff inside the room hidden by the cupboard

I'm having this problem too. I finished the Blood on the Ice quest, then bought the house and all the decor. I never had the option to "clean up the murderer's mess." Now I have a house all covered in blood and body parts. Halp!

I have this problem too with one of my saves. My guy trips over bloody parts and they get sent flying around. Also, when you run into items like this it sometimes sends your character into random directions very quickly running into walls.. it looks like it makes you teleport. It's ridiculous. If I spend that much money on a home I would prefer the blood and bones to be gone

Only way to get rid of it is to buy the cleanup BEFORE buying the upgrades.