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?
Suggested correction: That's not what happened or what was said. Daniel suggested Apophis and Klorel used the rings after he did, not that they used the Stargate after him. In "The Serpent's Lair", we see Apophis and Klorel use the rings BEFORE Daniel uses the Stargate. But we don't actually know how much time is meant to be left on the C-4 when they use the rings. They ended up using the Stargate before Daniel did and they never cut to them on board after Daniel escapes.
Plot hole: The last two invisible aliens are in the room with Charlie and "Mother". Since both of them can see the aliens, why don't they warn O'Neill that they are there?
Touchstone - S2-E14
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.
Touchstone - S2-E14
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.