Okay, so instead of helping Goodsprings at the beginning of the game, I decided to go talk to Joe Cobb (I think thats his name) about helping to take over Goodsprings with the Powder Gangers. I killed Ringo, gathered the items from Doc Mitchell and the shop owner, and ran back to talk to Joe Cobb. The quest "Run, Goodsprings, Run" got under way! Me and the Powder Gangers were walking towards Goodsprings, killing the good people of the town as we went (like I had done many times before). Only THIS time, all of the Powder Gangers stopped dead in their tracks after everyone was gunned down and would NOT move. I tried talking to Joe Cobb and all he would say is "We're busy killing these people...can't talk right now" or something to that effect. As far as I could see, we already gunned everyone down that was supposed to be gunned down. I mean, there was no one left to kill.

I went inside the shop and the shop owner says in a panicked voice "I can't do business in the middle of a gunfight!"

I went back outside and still...no towns people were left alive and the Powder Gangers hadn't moved. The quest was still active in my Pip-Boy...so naturally, I began saying "WTF?".

I see my quest arrow in my radar. I bring up my Pip-Boy, check the World Map, and here is my quest arrow for "Run, Goodsprings, Run" on the other side of the map, near the vicinity of Black Mountain. So, again, I exclaim "WTF?". I check my gear and begin the long trek to Black Mountain so that I can complete "Run, Goodsprings, Run". As I get closer to Black Mountain, I notice my quest arrow is blinking closer to Hidden Valley than Black Mountain. I get to Hidden Valley...and there, stuck inside of a ROCK, with only a rifle barrel sticking out, is Sunny Smiles, yelling at me and telling me to quit hiding like a coward! Again...WTF?!?!?

I try shooting her. No good. I try a melee weapon. No good. Sunny Smiles is well protected inside her little rock fortress she found for herself. She is literally STUCK inside.

Now, a rational minded person would say "Forget this quest...I"ll just start walking to Primm for my next quest and be on my way". But now, I"m pissed off. SUNNY SMILES MUST DIE!!! I travel back to Goodsprings, buy all of the dynamite I can get my hands on, go to the NCR Correctional Facility, snag all of the dynamite I can get from there, then I return to the rock in Hidden Valley, where Sunny Smiles is still safely tucked inside her rock.

26 thrown sticks of dynamite later, Sunny Smiles dies and my quest pops up as completed.

If I hadn't read further down, I was going to say have you found Sunny Smiles since she bugs out during that quest.
Thats bug is already documneted on the wiki under that quest.

Some NPCs will spawn in the middle of the map for unknown reasons, the one thats done it with me is Loyal but he's been normal since the latest patch.