Deliberate "mistake": Dr. McKay repeatedly mentioned how they would only have a connection between the Pegasus Galaxy and the Milky Way Galaxy via Stargate for 1.3 seconds. Yet when the Milky Way galaxy is dialed, the wormhole lasts approximately 11 seconds.

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?