Plot hole: General Hammond is promoted to 3-star general and command of the SGC is given to General O'Neill before the Atlantis gang even left earth. Why is it, that none of them find it the least bit odd that a 2-star Hammond greeted their return instead of O'Neill?
Suggested correction: The dream-state induced by the aliens had some ability to stop them from questioning their reality. (One of them takes quite a while to realise that a friend they're partying with died years before they left for Atlantis). It's not infallible or entirely consistent, but it would theoretically explain this.
Plot hole: In the episode "Where's the Wizard?", when Pim gets the Wizard from Lil' Danny, she holds it in her hand. When Lil' Danny steals it, he takes it out of Pim's backpack, meaning it must be Pim's Wizard. But when Phil points it out, she says it's hers. This could be a character mistake, but if it was Phil's Wizard, they would not be able to track the one Hackett had, because inputting the signal of Phil's Wizard would do nothing.
Graduation Match: Part 2 - S1-E52
Plot hole: When Zane has Cyber End Dragon attack Rampart Blaster, Jaden activates De-Fusion, allowing Rampart Blaster to be sent back to his deck (and allowing Burstinatrix and Clayman to come back to the field). Later, when Jaden summons Shining Flare Wingman, he states that it will gain 300 points for each Elemental Hero in his graveyard. We are then shown eight Elemental Heroes in his graveyard, including Rampart Blaster, but this card was never sent to the graveyard, it was sent back to his deck. (00:09:13 - 00:14:43)