I noticed on my first playthrough that if you talk to G0T0 about Vogga (he warns you not to deal with Vogga, as it'll weaken the republic: you get influence with G0T0 if you say you'll consider his advice), you CAN'T finish the New Fuel Source quest. I only got the "I notice G0T0 isn't with you" dialogue, and the only reply was something like "you're not as funny as you think".
The only way I could complete New Fuel Source was to talk to Vogga immediately after I blew up G0T0's yacht and talk to the Jedi Master, where I got the "He's not with me but will not bother you any more" dialogue option.
Same here.
Yeah, i could only finish the quest by [intimidate]-ing the Exchange Thugs, then saying "no, you wanted a fight, you got it", and then taking the DS points. Sometimes, though, the "You've cleared a path for Lootra's wife" note never shows up and I couldn't free her from the Refugee Sector.
It seems to be a bug based on your location once the battle's done. When you sheathe your lightsaber(s), that triggers the end of combat and you can talk to people; sometimes the "You've cleared a path" note showed up while I was running back to Lootra's wife, but sometimes it'd only show up if I stayed near the corpses of the Exchange Thugs after I killed them.