Continuity mistake: When Chazz is standing on the Slifer Red dorm roof and says Jaden didn't see the Society of Light, Syrus and Hassleberry can be seen standing on the ground at rotated angles. When the shot cuts to them, they appear to be side by side, and not rotated at all. (00:01:15)
Continuity mistake: When Jaden first meets Neo-Spacian Aqua Dolphin, in the shot of Jaden saying he's in Dolphin Heaven, only Aqua Dolphin's head is visible above the water. In the next shot, his shoulders are suddenly above the water as well. (00:06:27)
Continuity mistake: When Jaden thinks he is in Dolphin Heaven, Neo-Spacian Aqua Dolphin says "No, but not a bad guess" and raises his right hand out of the water. When the shot cuts, his right hand is suddenly back in the water again. (00:06:30)
Continuity mistake: When the crashed satellite is first shown, there is rubble shown next to the satellite and the Kaiba Co Ltd can be seen on the satellite, positioned to the opposite end of the rubble. A couple seconds later, when the lid to the card capsule falls off, the logo is now positioned on a different side of the satellite, closer to the rubble. (00:09:28)
Continuity mistake: When Jaden runs over to the crashed satellite, there is a close-up of the Kaiba Co Ltd logo that is covered in dirt. In the next shot, the dirt has disappeared from the logo. (00:09:34)
