Factual error: Anytime a character fires a missile at an airborne target, it's invariably from an M136 antitank launcher. The M136 is designed to hit relatively slow moving ground vehicles and is useless against fast moving airborne targets. (This is because used M136 tubes can't be reloaded and are very cheap to use as props).

Factual error: Season 4 Episode 16 "Trio": When Sam breaks her leg, Dr. Keller discusses with McKay the possibility of internal bleeding, then returns to splint her leg and offer her some ibuprofen for pain. A doctor concerned about internal bleeding would never offer a patient ibuprofen, as it inhibits blood clotting.

Continuity: In Season 5, Episode 11, "The Lost Tribe," when the Wraith have taken over the Daedalus, Dr. Keller's hair changes from being wavy to being completely straight and back to wavy.

Plot hole: Why do Dr. Beckett and Dr. Keller use so much Earth medicine? The Go'auld and Asgard both have devices for nearly instant healing and the Ancients are far more advanced than either of them. While they might be reluctant to use sophisticated machines to perform surgery or treat disease, things like cuts, bruises and broken bones should be easily fixed. And we know such machines exist, the Go'auld developed their sarcophagi on just such a device.

Continuity: In the second season, episode "Condemned", in the beginning when the crew is in the jumper, Ronan Dex has his hair tied back. When they land on the island and walk into the camp, his hair is down, and then they have to run back to the jumper when the prisoners start shooting at them. When they get back in the jumper, Ronan's hair is tied up again.

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.

Other: In the third season, episode "Phantoms", the crew members are in a forest having hallucinations because of the wraith machine. Sheppard is hallucinating that he is in the desert during the war helping an injured soldier, so when he's walking around why isn't he bumping into trees? He sees nothing but sand, even mentions it at one point, but they are in the forest and he walks around pretty freely.

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.

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

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?

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.

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?

Continuity: In the scene where Michael is first introduced to his quarters, he goes to pick up a picture of his parents. In the first shot, the laptop next to the picture is closed, but in the next shot through the security camera, the laptop is wide open.

Revealing: When they are escaping in the beginning of the episode, watch Rodney dial. As he finishes, one of the DHD address panels pops out and falls off.

Audio problem: McKay is talking to Sheppard about the differences between himself and Rod, and at one point says that maybe Rod screwed up and was chosen for "a one-way ticket to another universe", yet his lips form the word 'galaxy'.

Continuity: When the Atlantis team finds out that the experiment has caused problems in another universe, McKay's sister says to Rodney, something like,"You said that the chances of connecting to another universe that was inhabited were astronomically small." It was in fact Carter that said that.