My windhelm home is filled with bones, blood and mutilations. I upgraded it fully, and there is a necromancer table in one of my rooms. Is this a glitch or are other people having this problem?

You have the same bug I do. If you don't purchase the clean up option first than it bugs out and you can't purchase it.

Awh, its a pretty cool house. Oh well. I guess I will remain in my solitude, markarth, riften, or whiterun house for the time being until it is patched .

windhelm is a horrible city, destroy your house there!