After Lt. Col. John Sheppard says, "Is he supposed to be naked like that?", Hermiod says something in his native tongue. When played backwards, Hermiod says "These humans are infants." Later, after Col. Steven Caldwell says that they are still on course for the coronasphere, Hermiod says, "The incompetence of these humans is beginning to make me angry."
When Lt. Col. Sheppard is flying the F-302 and being followed by the virus-controlled F-302 he says, "I'm just gonna tap on the brakes." This is a subtle nod to Top Gun (1986). Tom Cruise's character Maverick says pretty much the same thing in a maneuver against a MiG fighter jet.
When the virus takes control of navigation, it flies to Daedalus toward a star where extreme radiation would kill the crew. In Greek mythology, Daedalus and his son, Icarus, were imprisoned by King Minos. They escaped using artificial wings made partly of beeswax. Daedalus warned Icarus against flying too close to the sun, but Icarus ignored the warning, the wax melted, his wings fell apart and Icarus fell to his death.