Continuity: When they first arrive on Teyla's planet, the DHD is close to the gate. When the wraith attack, the DHD is much further from the gate.

Continuity: Right at the end, after the entity has gone through the gate, we get an overhead shot of McKay lying on the ground in front of the gate. His legs are stretched out straight. In the next shot, one of his legs is bent. He's unconscious, so he shouldn't have moved.

Continuity: When they finally get through the gate by blowing the rear hatch (which serves as the exit ramp when open), they arrive on the other end with the ramp closed. Submitted by roboc

Continuity: Right at the beginning, the crew of the jumper only dials five symbols into the DHD before hitting the engage button. Submitted by Christoph Galuschka

Continuity: In the scene where the Wraith attack on the Mainland, Sheppard is stunned and falls with his right hand on his gun near his hip, but when McKay and the other guy grab him, to pull him to the gate, both the gun and his right arm are above his head.

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? Submitted by Grumpy Scot

Revealing: When the team first lands on the Planet and fist step out of the Puddle Jumper, you can see multiple footprints going in and out of the puddle jumper from previous takes.

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. (Time)

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? Submitted by Grumpy Scot