I believe all you have to do is loot the bodies during daylight as there is a bug that prevents looting during nighttime.
I have a similar problem that I'm going to post here in hopes that someone can help me. After receiving the quest, I encountered the thugs and looted the key from them. I then proceeded to the building where the thug leader is supposedly at, however I had previously lockpicked the door and found nobody inside before receiving the quest. So now that I got the quest, going inside the building there is no thug leader, there is only two npc's that don't have any dialogue options other than being able to "peer into their souls."
So now I can't complete the quest because the thug leader isn't even there.
Did I screw up being able to progress this quest by lockpicking the door beforehand?