In my newsest game, with hearthfires and dawnguard installed,
I used for the first time the companion command ''take items from containers''
the reason was a massive transfer from my bedroom in winterhold college
to my newly built windstad manor

being paranoid, I had saves at each step of the construction and transfer
so when puting a sword on the weapon rack showed ''stolen'' in red
I got suspicious. I never steal anything !!!

Sure enought throwing the transfered items out of each containers showed them all as stolen
Some items were not tagged because I had put them there myself before

I backtracked step by step until I found a save without that problem

Sure enought it was the save before I used the companion to transfer one whole winterhold closet at a time
(every closet in the bedroom was one step ... about 5 closet containers in that winterhold player bedroom)

I put asside those saves in a separate folder and proceeded from that safe point
I transfered everything manually the old fashioned way
I did use my companion to carry stuff, but by using the dialoguef
Everything worked smoothly, nothing was tagged as stolen this time after carefull verification

when I said the bu caused everything transfered that way to be tagged as stolen, I mean it
every tiny ingredient, food item, armor piece, soulgems...
every single thing was tagged as stolen

throwing everything out of the containers would sometime generate multiple piles, not all of which were stolen
but that's because, as I said, I had put some stuff myself that I had on me before from adventuring
I verified to a reasonable extent that onky that stuff was not tagged (mostly some ingredients, and a bit of ore)

well, I hope you fox that eventually, it nearly ruined my game
so much for trying out a feature !

there are false report out there that this is a hearthfire bug only
I don't think so. I think peoples used the companion take closet feature to move to their manor
they just forgot to mention it.

anyway, in my case it was verry clear and thoroughly tested.
easy to replicate.

I'm sure you'll get the same problem transfering to any player house or even dropping it on the groupd after taking it from the companion
(I didn't test that, my only interest was finding the cause)

to confirm the cause. I did repeat a closet transfer using the feature and had the same issue (items tagged as stolen)
then I did it normaly with dialogue and had no issue that time