Champion or Chazz-Been? - S2-E2
Revealing mistake: After Bonaparte has introduced Reginald, it cuts to Jaden, Syrus, Alexis and Crowler sitting in the seating area. On the third row are two Slifer Red students. The first is looking at his cards, while the second is looking at the first student's cards as well. Later on, when Reginald has Gilford the Legend attack Chazz, it cuts to Jaden saying "Here we go", and those two students are in the exact same position, looking at the cards. Clearly the same animation was reused on both occasions. (00:03:58 - 00:11:03)
The Hands of Justice: Part 1 - S2-E50
Revealing mistake: Right before Chancellor Shepherd briefs the students about the tournament, there is a shot of Obelisk Blue and Ra Yellow students around the outside of the building. Later in the episode, after Zane gives his medal to Blair, the scene cuts to outside Duel Academy, and the exact same shot of the Obelisk Blue and Ra Yellow students has been repeated a second time. (00:02:48 - 00:08:45)
Revealing mistake: At the start of the duel, in the shot of Alexis saying "If you give me the key now...", the Society of Light dorm members can be seen sitting in the seating area in the background. On the front row, there appears to be two students merged into one seat. (00:11:50)
Don't Fear the Reaper - S2-E39
Revealing mistake: After Jaden summons Dandelion in defence mode, he places a card face down. When he goes to insert the card into the slot on his duel disk, his hand doesn't appear to align with the duel disk. His hand appears to pass over the spherical red light on the duel disk, and not the card slot. (00:13:02)
Revealing mistake: While Syrus and Hassleberry are calling for Jaden, there is a shot of a cliffside, that then pans upward to reveal the back side of the Slifer Red dorm. The windows on the left side of the dorm appear to have been drawn wrong, as they are smaller than the windows on the right side, even though they are all supposed to be the same size. (00:00:03)