I'm guessing either its a script issue or the game still isn't fully fleshed out in this respect. I won't get into details because of spoilers but there are several locations in the game were you can't loot from enemies bases that you have cleared or NPC's that are no longer living in certain areas that are completely empty that you still cannot loot from without losing karma. No idea why you lose karma in certain areas in the game that are clear of npc's. This has to be the only complaint I have towards FNV.

I would be Jesus right now if it wasn't for that. You would think any group that is 'Hated' or 'Vilified' you wouldn't lose karma from killing them(SELF DEFENSE :gun: ) or taking their items stashed in crates and footlockers or just plainly put on a shelf(they're dead and they hate you :poke: ) so putting it bluntly I don't get why you should lose karma for killing and looting the ENEMIES. Okay so, here's a little complaint I guess you can say.