Just finished my last play through with what I consider my "real" SS, the one I'll take through all the DLC and such. I went with the MM ending and wiped out what I see as the three troublemaker factions. I've completed every possible non-radiant quest, so now I'm just in exploration and goofing off mode until DLC comes out.

I wander over to the airport (now that the fire has gone out) and decide to poke around the wreck of the Prydwyn to see if there's anything worthwhile there. Standing alone in the middle of the rubble and the burnt out airship frame, without a smudge on her, is Dr. Madison Li. She was non-hostile so I figured let me engage her in conversation.

"Being the director is a grave responsibility, I hope you're ready".

"I don't agree with Father's decision, but I'll abide by it."

"We'll win this with Elder Maxon."

Um, Doc, both those men were shot to pieces and then blown up, by me. Didn't you feel the earthquake?

I know this is just an artifact of Li having a very small store of dialogue to draw on but it made me laugh. It's as though she's just wandering around, shell shocked, unable to process that I nuked both her employers.

Huh. It's weird that she appeared at all.

Looks like the game couldn't handle someone having Li leave for the Brotherhood and then destroying the Brotherhood