When Sheppard was beamed out of his F-302, he was sitting down. When he re-materialized, he was standing up.
When Sheppard flies out of the bay to get the last "flyer" on the outside, the bay doors open, but the virus had already locked those doors open.
It's never made clear how the virus can instantly return when the system is purged. It should take time to make It's way through the system again.
From the start, there is a huge hole in this plot: f Dr. Weir, Lt. Col. Sheppard, Dr. McKay and Dr. Beckett are all aboard the Daedalus, who is minding Stargate Atlantis Headquarters? Only Teyla, an alien to Earth, is left there. On many occasions, superior command members have expressed concern over her even being left alone, much less in charge (by default).
When ordering the ship to move off at sub-light speed, Colonel Caldwell refers to Captain Meyers (the pilot) as Major.
When talking about the candidates to join the Atlantis team, Dr. Beckett describes one of them as a graduate of "John Hopkins". The University's name is Johns Hopkins.