This is what you get for killing everyone you see.
On the one hand, that's kind of true. On the other hand, it's a little more than just that, imo. <_<
I'd read about the darn problem (only in a general way tho, not specifics) and I still caused it. I think it really is a matter of play-testing not taking different playstyles into account.

1-I don't use VATS, I shoot in real time. After the start scripted fight scene, I kill these two baddies guarding a bridge, so I'm already in combat/ambush mentality. I start crossing the bridge, and halfway across someone on a high rock starts shooting at me. This guy is FAR AWAY I can barely see him, all I know is he's shooting me with some auto-weapon that's giving me pain (I'm very low level w/no big weapons, btw). So I shoot back and start backpedaling to find cover. Remember I'm not using VATS, so I see nothing but a distant little dude shooting at me, no names.
2-The shooter drops off his rock to chase as I back off. So I'm guessing the named NPC who shows up a couple seconds later also drops off and gives chase. This meant, in the heat of "combat mode", that I thought he was another enemy coming to help his buddy, so I just shot in their general direction, hit both, and Mr. Friendly goes hostile/red (I never noticed he wasn't red to begin with, he's so far away plus I'm focused on trying to hit the first guy). I keep the GUI very faint so in mid-battle didn't notice the Fail quest message (my fault keeping GUI like that)
Luckily I wasn't too far into the DLC before I thought to dash forward and check re:the issue and yup...restart. And in the restart I hit the guy
again, since I didn't realize what had triggered it the first time, but this time he got close enough for me to see he had a name so I restarted again. Bah. LOL