This is a side effect of the fact that you can join so many factions. If you were friendly with that Powder Ganger, you'd be stealing those items from an ally. The problem is that coming up with a reasonable way to have the ownership flags switch depending on your group reputations is kinda tricky.
true,what they should do is flag them all green and make sure they are line of sighted,that way if you are not seen by anyone but god herself then no bad karma should be added.
theres a few places where it makes no sense to have red flagged items,especially in an enemies base etc.
i`m still not sure if bad karma is added at times when it moans at me when i am stealthed and unseen.
but never fear,i have a feeling the modders might just fix it one day.