• The name of "Shrink" was "Collapse".
  • the card Bright Castle only works on one of your monsters not all them
  • The name of "Sage's Stone" was both Sage's Jewel (in the menus) and Sage's Stone (on the card itself).
  • The name of "Aqua Chorus" was both Aqua Chorus (in the menus) and Blue-Eyes White Dragon (on the card itself).
  • In all versions of the game Pegasus disappears from one city after a player clears the first half of the game. In the European version he properly reappears in the other city during the second half, but in the North American and Japanese versions due to a glitch in the programming he never reappears. Therefore it is important to get his deck recipe and to get "Imperial Order" in a trade from him while he is still available since it is the only way this card can be obtained.
  • When your Two-Man Cell Battle is activated in a duel with Bakura during his turn, Bakura never decides whether to use its effect, and the game cannot continue.
  • The AI of the game misunderstands the effect of "Solomon's Lawbook". They will often activate it during your turn when you have a card such as Dark Snake Syndrome. The AI is under the impression that the card can skip their opponent's Standby Phase as well as their own.
  • When you activate Blue Medicine, although the card lore said to "Increase both player's life points by 400", it only increase the controller's life points.
  • Horn of Heaven cannot be used to negate the special summon of a monster.
  • During the Expert Cup, when viewing Joey duel Yami Bakura, even when Yami Bakura won, this duel counts as a loss for Yami Bakura, and it goes on your own record. The same thing applies when Yami Yugi duels Seto Kaiba, even when Yami Yugi won, it counts as a loss for Yami Yugi, and it goes on your own record.
  • When you first meet Marik using the fake name of "Namu", he introudces himself and says "My name in Namu", instead of "My name is Namu".

  • If Insect Barrier is active and you use DNA Surgery to change your opponent's monsters into insects during your opponent's attack, the monster attacking is able to finish its attack
  • If Dangerous Machine Type-6 activates and the die lands on a 5, nothing will happen.
  • A large number of fusion monsters and other miscellaneous cards are inexplicably absent from the game despite the game going all the way to cards from Flaming Eternity.
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