Went into the ruins, found the hostages, talked to the Khan leader and proceeded to kill the Khans. The last Khan was injured badly and ran towards the NCR in the ruins, they shot him while I was reloading (I think this is where the game got screwed up). Freed the hostages.

Now the guy that gave me the mission outside of the Boulder City ruins only says "There is no time to talk, there are still Khans alive." even though they are all dead.

Savegame: http://hashers.ca/quicksave.rar

I had a similar experience until I checked and the quest wasn't my active quest. I changed it to be my active and the quest objective arrow pointed to inside the building where you converse with the Khans. There was still one left inside there, mopped him up and the quest completed. Is the quest still in your pipboy? If so, make it active and see if there's any objective arrows still pointing around.

I'd check your savefile, but I'm way too paranoid for that.

I just double checked: it is my active quest in the Pipboy and there is no location associated with this quest on the map. I also have ED-E with the crazy sensor range. If there was any enemies left over I would see them.

Yeah I can't finish this quest either. It's pretty annoying. I don't have a save file before I chose the option to just run in and light everybody up either. I kill 4 Khans, loot them, free the hostages, and continue on to talk to the Monroe and he just tells me there are more Khans left.

There's more than 4 Khans. There's 2 more inside a building that's instanced.