Personally, I think it's pretty obvious that Liara was mind-controlling Shepard ever since she went all "EMBRACE ETERNITY" on his ass, manipulating him into serving the goal of galaxy-wide Asari supremacy by pointing him at their enemies, giving him visions of some made-up invaders, and feeding a god/martyr complex in which he was the only one who had the conviction to do what needed to be done, and everyone who saw through his lunacy was just blind to the real threat. There's no denying this unless you didn't play the game or weren't paying attention; I mean, it's RIGHT THERE. The plot holes and inconsistencies surrounding everything to do with the Reapers, hints throughout the series that Asari are constantly mind-raping other species and messing with their perceptions, Liara's manipulative nature as demonstrated in ME2, everything.
Still haven't heard anything that contradicts this.