That depends, what all did you change? Is your target near/in goodsprings, and are they in an enemy faction? That would cause everyone to attack them.
i completely stripped factions out and started again! i made the target NPC a "wastelander" or something, even made that faction allies with GSfaction!
so basically i dont think its factions? the NPC is in the GSAbandonedshack cell, which isn't really in GS tbh....