Holy crap I've had a ridiculous number of plot flag bugs on my second playthrough, and I had none at all on the first one!
The plot flags for companion quests seem to be sensitive to a few things:
-how fast you max friendship or rivalry
-how often you use or do not use a character (this may just be a coincidence)
I had Merrill to 100 Friendship at the middle of Act II,
before I completed her romance quest--I was trying to max her out so I wouldn't gain rivalry points when destroying Tahrone's "evil tomes."
And it
completely screwed up her Act III personal quest (A New Path). I received the completion dialogue upon doing the usual "talk to a character at the beginning of each act" quest. I used the dev console to reset the plot flag and finished the quest properly so I could get the loot and XP.
Now she always asks to visit her old house in the Alienage every time I right-click on her outside of my house. It's like the game's stuck, since it already completed the end dialogue of A New Path.
Additionally, I've gotten
none of Fenris' personal quests at all! None of the flags have been raised, and I haven't found any of his gifts or anything, so I'm missing all the loot/XP from his personal quests.
These bugs are worse than the worst bugs from Origins... *facepalm* Though the frequent crash-to-desktop and memory leak related framerate tanks in Origins weren't exactly welcome, they didn't break entire quest lines.
