Plot hole: Huge plot error: Apophis and Clorell (Skara) should not have survived the explosion in Season 2, Episode 1 (when they attack Earth with two ships). In "Family" they explain that Apophis and Clorell survived by escaping through the stargate aboard Clorell's ship moments after Daniel Jackson did the same. However, when Daniel Jackson escapes through it, Apophis and Clorell are not even on the right ship, and there is 1 second left on the C4 timer when Daniel escapes. They actually show Daniel Jackson escape, and then cut to Apophis and Clorell still aboard their ship. So apparently, Apophis was able to "ring" from his ship over to Clorell's ship, make it to the stargate room, dial an address, and escape through the stargate all within literally 1 second. Is this guy related to The Flash?
Character mistake: The team are finding out who could have stolen the weather device from Madrona and find an energy spike at the same time SG2 are on a mission. "But SG2's mission is galaxies away from Madrona" Says Teal'c. At this time the only missions the teams could go on was in our own galaxy and couldn't be galaxies away.
Plot hole: When half of SG-1 return to Medrona to detonate a charge aimed at the gate, why didn't they just go to another planet? As when they went to Medrona, there was a blizzard going on and they also had the natives saying they will arrest them as they still hadn't returned the Touchstone. Could have just saved themeselves some hassle.
Plot hole: The NID guys escape because Jack can't kill them. He fires his MP-5 around them to try to make them stop. Is there a reason he didn't bring a Zat gun along? The whole point of this mission was to stop the NID rogue agents without killing them and to capture them if possible. The Zat gun seems tailor-made for a mission like this.
Character mistake: When Hammond and Carter come out of the base, Hammond is told he's been gone 22 hours. Hammond says he's only been gone about 20 minutes. To which Carter says, due to time dilation, time is moving an average of 600% slower and that telling O'Neill to wait 5 minutes would be 6 hours or more. However, 600% is just another way of saying "6 times" and time is slower by about 66 times, so she should have said an average of 6,000%. 5 minutes being 6 hours would be 72 times slower.