ok im stuck in flying blind now lol i have follow the quest line power up the generator and everything access the weapon storage and then my game crash get back on the game and the power in the bunker is off the door is closed again and i cannot power up the generator again to go finish the quest 
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Running into this issue as well.
Opened the doors before getting the key and couldn’t complete it. I read somewhere that going in with co-op would allow you to complete it, but when I did that, I ran into your issue: locked door to the gas filled room even though I have the letter/key in my log files. Tried switching the generators on again too. Kinda bummed about that.
It’s good these issues are posted, for @ProntoManagement to be alerted to.
Vanilla version had bugs like this that were corrected in their first patch. Hopefully this will be corrected as well.
Yes I have the same problem. I lock-picked the doors to the inner weapon room and then picked up the key. This made the quest stuck as not completed. And still is after the last big update.
Went back to see if it was fixed after the last update but the doors to the weapon room is locked and there was no way to open them again.
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