This episode takes place at the same time as Stargate: SG-1 Season 8, Episode 9, where Brigadier General Jack O'Neill is in command. In this episode, Major General Hammond, who was previously promoted to Lieutenant General, is in command. Everyone on the Atlantis team knows this so the memories that are accessed by the "fog" entity should reflect this. The characters that returned to Earth should have noticed this immediately and realized that something was wrong.
An external shot of Major Sheppard's bachelor pad shows a flagpole with a Canadian flag on it. Being that Major Sheppard is an American, he would not have a Canadian flag outside his home.