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!
