Continuity mistake: At the end of the battle between Jaden Yuki and Gravekeeper's Chief, just as the explosion settles, in one shot you see the Gravekeeper's Spear card to the left of Gravekeeper's Chief on the duel disk. However in the next shot Gravekeeper's Spear is replaced with Magician of Black Chaos, which Chief neither has in his deck or ever played in the match.
Other mistake: Syrus summons to the field Drillroid and has it attack the Gate Guardian in defense mode, but is blocked by Defence Wall because of its effect, and Defense Wall is destroyed. Because of this, Jaden and Syrus lose 500 Life Points. While it does seem logical that their life points would go down because Drillroid has 1600 attack points and Defense Wall has 2100 defense points, they should not lose life points in the first place. This is mainly due to the fact that Drillroid's effect causes a defense position monster to be destroyed instantly, without losing life points. If Drillroid was capable of destroying Defence Wall, then their life points should have remained at 1700.
Continuity mistake: In the opening scene, Crowler is frustratedly walking through the corridors of the academy and walks past several Slifer Red students. In an overview angle, there are 5 students, with two of them standing by a door to the left of Crowler. In the next shot, Crowler is shown walking past the door, but there is no sign of the two students.