Ok, so you guys know the Faustin in Riverwood that can be your companion? Well when he was with me, he died, so I took over his house. But when I put my loot in his cupboard and dresser and chest, later that day (like the second time I came back to put more stuff in) some of the objects i put in were red (the name of the object) When I took one out, thinking that it was stealing, it didnt say anything. But it's my stuff, why would it be stealing?

When you say you took over his house, you mean like you simply moved in? Because the game doesn't really reckognize you killing someone and than claiming their house, you usually have to purchase a house or gain the house through story oriented gameplay. So while you might have moved in, you might not legally own the house yet.

Well I didn't kill him myself (a bandit did lammme)
but yeah, guess i have to move out :'( isthat stuff always gonna say its stolen from now on because that would svck

edit: I see what you are saying, but its not like the items i put in were stolen. They were all items i got fairly. I guess it just didn't like me putting them in his house

at the same token, why wouldnt all of the items be red then

Just take anything you want. Unlike OB the vendors will not know that you stole the items.