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.
Plot hole: After Zelenka is finished with his description of how Atlantis rose from the ocean, Ford asks him if he said anything that would require security clearance to see. But if he is worried about security, why did he film Zelenka sitting in front of a top-secret Naquadah generator? This would be the equivalent of a soldier filming Enrico Fermi (speaking in Italian) in front of a nuclear bomb prototype then asking if he said anything secret.
Plot hole: In early episodes, when Sheppard and his team are attempting to capture a Wraith, they ambush him and his soldiers with tasers. The taser just irritates the Wraith. Why don't they have Zat guns? (The real reason, of course, is that Wraith stunners will be introduced in 2 or 3 episodes.) But it makes no sense to not bring such a useful non-lethal weapon along into unknown territory.
Suggested correction: Production-wise, Zats are a part of SG-1 and Atlantis should have its own "look and feel." In universe, it's probable that the SGC doesn't have that many Zats (they can't make them so every own they have has to have been captured at some point) and therefore wouldn't want to send a load off on what was thought of as a one way trip when the Atlantis Expedition first left. Plus there would be no guarantee that the Expedition would find any way of recharging or maintaining them once they got where they were going.
Plot hole: Why do Dr. Beckett and Dr. Keller use so much Earth medicine? While the Ancients may have evolved past disease and genetic defects, they would still need treatments for physical injuries. And we know such advanced medical machines exist, scanners have been shown on screen and the Go'auld reverse-engineered their sarcophagi from an Ancient device. While they may be reluctant to use unknown machines for surgery or disease, surely bruises and broken bones should be healed instantly!
