Ok not once, but twice now, I've had a game-stopping bug occur due to a very simple concept that should never have seen the light of day. Faction cutoffs without warning. Quests automatically put into your questlog without your acceptance of them. Those quests just by existing in your log then bug out your relationship with a faction (railroad). Twice.
First when BoS wants me to wipe out railroad, then when Institute does the same. How did this get past testing and who the F thought this was a good idea in the first place... Talk to captain Kells and all the sudden I couldn't even get Ballistic weave. So I do the sensible thing and wipe the BoS off the earth. Then I can't warn Desdemona after Father puts a quest into my log (even if I don't actually), either because of the events above, or just because the game is buggy.
That's twice Des was my quest marker and would not respond to the quest at hand. How. The. F.
And a fix wasn't even in the recent patch!
If you need more info about this, just google fallout "warn desdemona".