It is a good idea to run this game on a series of manual save slots. In past games I could fix any quest glitch by reloading a save point from before I started doing the quest and it would sort out the second time around. As you have seen.
Have a save slot from before you start on the quest. Go ahead and accept them as you get them, but when you start doing something for the quest, create the slot or use a manual slot you already have
One or two slots for during the quest (mostly so you can undo a decision if needed)
Then if all is well, another slot so you don't have to worry about the quest
Finally do not rely on autosaves, they will paint you into a corner sometimes.