So I went into my house in Whiterun today to drop off a few Dragon Bones and Scales and found that all of the ones I currently had in my chest were red, and when I take them out of my chest they pop up as stolen. Totally awesome since I just lost more then 50 Items, unless I want to sell them and buy them back.

Are you sure that you don't happen to have one item in that stack of 50 that you really did pilfer?

If one of them is stolen, just looking at the stack shows that it has stolen contents but that doesn't mean the entire stack is flagged as swiped.

Have you ever threw them in the chest at the place you can stay at in Riverwood because that would explain why. I made that mistake but lucky was able to jump back a save and prevent that from happening.