So I saved Rugan and Ollie from the gnolls and perusaded Rugan to give me the shipment. I was looting the rest of the cave and spotted the shiny alchemist fire bottles sitting there. I took them, but got caught and was handing them back, but before the dialogue freeze I had clicked my character away and it counted as fleeing the crime when the dialouge ended. Rugan and Ollie got hostile and I knocked them out. 
After that I went to the hideout, said the password to get in and told Zarys I had saved her men. THIS was a big mistake I think, as it locked me out of the hideout when Rugan bugged. Zarys wont let me in before Rugan returns, Rugan will not leave his cave even though he says he will (I even bribed him so he would talk to me again). 
My theory is that the knockout is registered as a kill and now the only option to get some loot is to wipe out the hideout. 
I have long rested 3 times since the knockout. This is on Patch 8, no mods.