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?
Plot hole: Before the last chevron locks & the wormhole engages, Carter asks "Where's the iris" to which Hammond responds "Someone used a remote, whoever it is has our codes". All well and good, except without the wormhole being active, they wouldn't be able to receive the code.
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.
Plot hole: Anytime an SG member starts acting weird or something happens that is "impossible", SGC personnel always act skeptical about it. Considering what they have seen in the course of the show, "that's impossible" should have long ago fallen out of their vocabulary. And while I realize that Sam and Daniel are scientists, they have seen enough examples of incredibly advanced technology that they should be far more open-minded when looking for explanations.
Plot hole: When the team manage to create the cavern with the buried stargate they send Teal'c through to drill his way out, but wouldn't it be safer (and significantly faster) to fire a missile or two through and blast their way out? They have no idea how deep the stargate is buried, or under what type of rock, so sending Teal'c with only four hours of air seems suicidal. (00:35:00)
Plot hole: During the briefing at the Tok'ra base about the deadly symbiotic poison, Ren'al says that dying symbiotes release their own toxin which is just as deadly to the hosts. Yet in other episodes when a symbiote dies in the host's body, the host doesn't die, even without medical treatment. For example, the whole infected town of Steveston is just fine when all the symbiotes are killed (s06e05).
Plot hole: When the team manage to cause the cavern to form over the buried stargate they send Teal'c through, but shouldn't the cavern be a vacuum? Air doesn't travel through the gate and the stuff caught in the vortex is destroyed, so Teal'c wouldn't need an oxygen mask he'd need a spacesuit. (00:35:00)
Plot hole: And the end, when Vala and Mitchell activate the Stargate home, SG-1 is delayed in being able to step through because they are detained. However, the whole time they're detained by the gate, there's no radio transmission from SGC. Later we find out they're coming home early, so on SGC's side, they just had an unscheduled off world activation and would know it's from the planet SG-1 is on, and they would radio for an update. None of that was done so the conversation could happen.
Plot hole: The team go through the gate to disable a drone with the intention of being able to close the active Stargate, but once they go through in a submarine, the gate closes behind them, rendering the mission pointless. (00:24:18)