In my worldstate, the Warden (Origins) did not romance Morrigan, Alistair had the God baby with her, and the Warden stabbed her on their final meeting.
But in Inquisition, she said she romanced the Warden, had the baby with him, and stepped through the Eluvian with him.
This happened to me as well. I imported a female Human mage who romanced Alistair and they remained Wardens together after Alistair performed the Dark Ritual. It seems that the majors of my world state were reflected perfectly well everywhere else. The codex, the storyline, Leliana, even Cullen all appropriately reference it.
Morrigan, however, insists that the HoF was her lover and baby-daddy. I could rationalise it by saying that sex with Alistair was so traumatic that she invented an alternate reality that exists only in her mind, but come on. It's way more likely that he'd be the traumatised one. 
All in all, since it was completely localised to her I guess it's not the end of the world, but it was pretty disheartening all the same to listen to her rattle on about a character that doesn't exist, especially since the whole point of the Keep was to untangle the mess of plot flags.