Plot hole: General Hammond is promoted to 3-star general and command of the SGC is given to General O'Neill before the Atlantis gang even left earth. Why is it, that none of them find it the least bit odd that a 2-star Hammond greeted their return instead of O'Neill?
Suggested correction: The dream-state induced by the aliens had some ability to stop them from questioning their reality. (One of them takes quite a while to realise that a friend they're partying with died years before they left for Atlantis). It's not infallible or entirely consistent, but it would theoretically explain this.
Other mistake: In Shepard's apartment, there is a fresh pineapple and other fruit in his kitchen. This despite him having been in Atlantis for several months. This later turns out to be an artificial reality, but that should've been a big hint.
