- You receive a Spell Counter even if the card that gains it was not on the field when the Spell Card was activated (i.e. if you summon a "Skilled Dark Magician" with "Premature Burial", it will gain a counter).
- Dimitri is able to pull of the fusion summon of "Alligator's Sword Dragon" with "Polymerization", "Alligator's Sword" and a "Sheep Token" (when all of his monster card zones are full).
- The effect of "Big Core" that places counters on itself when it is Normal Summoned activates when it is Special Summoned as well.
- When "Big Core" attacks your opponent directly, it will lose a counter, despite its effect stating: “If this card battles a monster, remove 1 counter from this card at the end of the Damage Step.”
- When you attack "Des Kangaroo" with a card like "Mother Grizzly", the effect of "Des Kangaroo" will destroy your monster. However, you will be able to activate the effect of your destroyed monster, as if it were destroyed by battle. (Unknown if this applies vice versa, with the AI attacking your "Des Kangaroo".)
- If you attack a face-down "Flip Effect" monster with "Drillroid", the monster will be flipped and immediately destroyed, without its flip effect activating.
- When the effect of "Elemental HERO Flame Wingman" activates, sometimes you will be asked to chain to that effect even when you cannot even activate anything at that time.
- If a monster battles "Harpie Lady #3", even if it is sent to the graveyard and summoned back to the field (i.e. Premature Burial), it still cannot attack for 2 turns.
- If a monster with higher ATK attacks "Injection Fairy Lily", "Injection Fairy Lily" is destroyed regardless of whether or not the effect is activated.
- An opponent's "King of the Skull Servants" revives without banishing a monster as a cost. So it can be revived countless times and is practically invulnerable to opponents attacks. (encountered in the duel with "Titan")
- Spirit monsters cannot be Special Summoned, but in this game this is sometimes ignored. For example, if your "Pyramid Turtle" is destroyed by battle and sent to the Graveyard, you can Special Summon a "Dark Dust Spirit" from your Deck. However, its effect won't be activated and it will return to your hand during the End Phase.
- After you attack a face-down "Winged Kuriboh LV10" and it flips face-up, the AI will Tribute it to successfully activate its effect during the Damage Step (regardless of whether or not it would be destroyed by battle)
- Attacking an opponent directly with "Sasuke Samurai #4" will be preceded with a coin flip. If you correctly guess the result of the flip it has a chance to destroy one of your monster including the attacking "Sasuke Samurai #4.
- When a monster that is unaffected by Trap Cards attacks your opponent's monster while "Astral Barrier" is on the field, the monster should attack the other monster. But, instead of that an infinite loop activates ending the duel there, unless you have a card to destroy the monster or "Astral Barrier". (someone clarify this please?)
- If your opponent has no monsters on the field, when you activate "Ojama Trio", then activate another copy of "Ojama Trio" in a chain, a total of 5 Ojama Tokens will be summoned to your opponent's side of the field.
- You cannot activate "Waboku" during your own turn.
- When you activate "Widespread Ruin", the face-up monster with the highest ATK your opponent controls will be destroyed, regardless of battle position.
- "Blue Medicine" only increases your own Life Points by 400, rather than both players' Life Points.
- You can activate "Burst Stream of Destruction" even if you don't control a face-up "Blue-Eyes White Dragon".
- If you chain a Quick-Play Spell to "Giant Trunade", it will be returned to your hand after it resolves.
- If you Set a monster with "Book of Moon" that was affected by "Limiter Removal", that monster will still be destroyed during the End Phase.
- The AI is capable of activating "Premature Burial" even if there are no monsters in their Graveyard. In this case, "Premature Burial" destroys itself when it resolves.
- Even if a monster that can attack more than once such as "Mermaid Knight" or "Cyber Twin Dragon", "The Dark Door" only allows that monster to attack once.
- If "Toon World" is returned to your hand, all Toon Monsters you control will be destroyed.
- If your opponent has used "Snatch Steal" on a monster equipped with "Big Bang Shot", when that monster attacks, both you and the opponent will take battle damage.
- If both you and your opponent have 1 "Snatch Steal" equipped to the same monster, and both copies of "Snatch Steal" are destroyed at the same time (i.e. "Heavy Storm"), control of the monster will go to whoever destroyed both cards, even if that player is not the original owner.
- The AI knows and will never attack a face-down "Marshmallon" you control.
- The AI will always try to use "Snatch Steal" on a monster you control with the highest attack, even if that monster cannot change control.
- If you have 3 monsters out on the field and attack a facedown "Hane-Hane", "Penguin Soldier" or "Man-Eater Bug", the monster that attacked will never be chosen as the target for their effect.
- The AI never attacks your strongest monster with their strongest monster if the battle would result in both monsters being destroyed by battle.
- If you have "Marauding Captain" and at least one other monster in your control, with equal or lower attack, the AI will not initiate an attack.
- The AI only returns his defense position monsters (back) to attack position afer he summoned another monster.
- If your opponent has a set "Torrential Tribute", they will be able to activate it to the Summon of a monster via an "Attribute Summoner", even though those effects are in the "Damage Step".
- The AI will activate "Ring of Destruction" even when this results in the AI losing the duel.
- On the duelist calender, instead of 11th, 12th, 13th, they wrote 11st, 12nd, 13rd.
- In the English adaptation of the game there are references to the Japanese version. For example: Syrus says that Jaden is like his big brother (That's how Syrus call him in the Japanese anime). Chazz's motto in English is "Chazz it up" while in the game is an English translation from the original Japanese motto, "Chazz Thunder".
- When you have a card that can be activated during the Battle Phase (like "Coffin Seller", "Call of the Haunted", etc.), and you inflict damage, in the trigger window will say: "You took damage..." instead of "Your opponent took damage..,"
- When attacking and destroying an Ojama Token with "D.D. Warrior Lady", its effect will activate. The trigger window will say: "Will you remove the card "D.D. Warrior Lady" and your opponent's monster "Flame Swordsman"?".
- When you Summon "Copycat" and its effect activates, the trigger window will say: "Select opponent's monster to switch ATK/DEF." The effect will still resolve normally though.
- When dueling Zane and he activates a Trap Card, he will say "Everything action you take is worthless. I activate my facedown card..."
- After the special midnight Duel with Zane (during the same day you acquire "Power Bond" from Syrus), Zane will tell you at one point in the conversation that follows, "And you play with cards well, Jaden," despite the fact he referred to you by your character's name before the Duel.
- After becoming the King of Games, the game will say "Congratulation" instead of "Congratulations".
Name and Lore Errors
- "The Dragon Dwelling in the Cave" is known as "The Dragon dwelling in the Cave".
- "Eternal Drought" is known as "Eternal Draught".
- "Warrior Lady of the Wasteland" is known as "Wasteland Amazon".
- "Stronghold the Moving Fortress" is known as "Red Gadget - Stronghold".
- In the description of "Reversal of Graves" description, it is written "...when there is 15 or more cards..." instead of "there are".
- "Shield Crush" is known as "Shield Crash".
- The effect of "Card of Sanctity" reads: Both players draw until they both have 6 cards. Despite this text, the card actually removes from play all cards in its controller's hand and side of the field as a cost, and makes them draw cards until they have 2 cards in their hand.
- The effect of "Fairy King Truesdale" reads: "As long as this card remains face-up on the field, increase the ATK and DEF of all Plant-Type monsters on your side of the field by 500 points." Despite this text, the ATK/DEF increase is only applied while this card is in face-up Defense Position.
- The text of "Inferno Tempest" reads: "When you take 4000 or more Battle Damage from one attack, you can activate this card. Remove all monsters in each player's Deck and Graveyard from play. These monsters cannot be used again during this Duel." Despite this text, the card can be activated in-game when its controller takes 3000 or more battle damage (and no less than 3000) from a battle, and the monsters removed from play by this effect can be used again during the same Duel.
- When you use a card that allows you to see the top card of your Deck, sometimes the top card remains face-up.
- When the screen is going very fast, you may see the back of the card instead of the front.
- When dueling Lyman Banner, he may activate 2 "Tolls". When you attack, the picture of 1 "Toll" would show up but the other one won't. The effect is still activated though.
- If you are playing in a match, when you exchange cards, the screen may freeze on you.
- When you try to read the description of all Expert Booster Packs, Dorothy goes into an endless loop of moving her mouth and not saying anything, forcing the player to shut off the game.
- When "Des Wombat" is on your opponent side of the field and you have a face up "Reflect Bounder" in attack position and your opponent attacks "Reflect Bounder" with another monster, both the effects of "Des Wombat" "Reflect Bounder" will cancel each others resulting in an endless animation loop and you will have to restart the game.
- "Respect Play" lets you see what type of cards your opponent has (Spell, Trap, or Monster) but not the actual cards themselves. However, you can see the opponent's cards if you have a face-down you can activate during your opponent's turn.
- If you chose to put "Spiral Spear Strike" and related cards into your Deck (Press L-Button while choosing "Spiral Spear Strike") the game freezes.
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