Hmm, he's my 2 cents to this novel of the thread(350+ pages!)
1. Reference to the moving walls: This ties into the audio log in ME2/disabled reaper mission, which could indicate indoctrination, either by the reapers or by TIM. Or it could be neither and simply the citadel resetting itself for the next cycle.
2. Kid in the vent during the intro: Ties into ME2/disabled reaper mission, where one of the scientist claims to have seen something in a vent(if I remember right).
3. Kid "teleporting" from the ground, up to the building, and back down again: Design error.
4. Smokey shadows during the dreams: Possible sign of indoctrination(ties with ME3/rachni queen)
5. Smokey shadows during the end with anderson and TIM: The indoctrination effect from TIM, who has limited control over reaper abilities.
6. 1M1: Nothing related to the story line. Unless I missed something, and 1M1 has a direct connection with the reapers or indoctrination, its mere presence doesn't indicate anything other than possible personal significance to the design artist.
7. pre-rendered cutscene with shepard in rubble: Doesn't look like the citadel to me, but other than the presence of concrete, I don't remember hearing any ambient battle, just electrical snaps. It could be in london, or it could be recycled from a cut ending scene.
8. Normandy getting hit with the blast wave, squadmates walk out after crashing: Continuity error. There were scenes cut from the game which show how your squad mates got back to the Normandy from earth.(See
http://social.biowar...index/9787569/1 and
http://imageshack.us...93/scriptw.jpg/ and
http://youtu.be/eBktyyaV9LY?t=2m35s ) and it's not space magic. If your ESM was high enough, the Normandy was supposed to blast harbinger with missiles... Or maybe it wasn't cut from the game and it is a hallucination

Either way, that was way more than 2 cents