I think I found an issue with faction alliances - specifically, I helped the Black Eels take out the Scrappers. That alone was fine, I wandered the rest of Junktown taking down stragglers after the main fight, Silas lived, and the quest completed; however, when I went to the casino on the north of town, I noticed the guards there were hostile. So I figured this was a Scrapper joint, and killed everyone there - all of the hostiles, that is, I didn't kill any of the gamblers who didn't attack.
Well, when I went back to town I noticed that the Black Eels were now hostile to me as well ... is this by design, or did I do something wrong? Or is there a faction bug in there?