SPOILERS: Oldest Trick in the book Quest killed my game

[</TraumaticAI>]

So I just got done confronting alex after killing everyone in the mine, or at least I thought I did. I was in mid-cutscene when a flamethrower guy came up behind me and basically instakilled (inside cutscene). I've respawned, killed the flamethrower guy and checked everyone is still dead. I go back finish Alex's conversation and the quest is still asking me to "Clear the mine of cultists" but they are all literally dead. (I've gone round and checked everywhere) I can't literally finish the quest and move on.

I've taken a break, Gone back in after a game reboot to see if I could re-trigger it and now the quest has gone and does not even exist in quest history or any markers on map, so can't continue this new campaign :( anyone got any ideas?

[Hakuso]

Seems they count the non-hostile guy as a target, I left him alive since he wasn't trying to kill me but eventually just put an arrow through his head and the quest advanced.

It also didn't let me advance without killing the leader, though the story I'm reading makes it seem like that should be an option... And the one I would have chosen.

[spoggie]

I had a similar problem killing cultists in the cave.
The first time I killed some too quick and three dead bodies still had markers active.
Fortunately I was able to quit, restart and kill everyone again.
...but the second time I made sure to let the foes become aggressive.
There was a non-hostile remaining so I punched her.
She turned hostile, I killed her and the quest advanced.

[Mooman]

I broke this quest and entire main quest by going in guns blazing... Alex ends up hostile but essential. When downed she can't be interacted with.

Reloading caused the quest to vanish with no way of restarting it... even talking to Audrey in the Vault does nothing...

Oh, well... It was my second character. Just follow the instructions and wear the disguise in the cabin and it should be 'fine'...