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: 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.
Stupidity: Characters repeatedly make note of how hard to kill the Wraith are, but sometimes, especially in the final episode(s) of season 1, they go down easily in a few bullets each, and then don't even regenerate as the characters turn their attentions elsewhere.
Suggested correction: It's explained that Wraith are easier to kill the less they've fed recently, and that in later seasons, with more and more Wraith waking up, fewer and fewer are getting chances to feed before they fight the Atlantis Team.
