Bug: When playing in Free Mode in Chapter 3, "Azog the Defiler", if you skip the cut scene that shows Azog killing Thror, the next area where Thorin is supposed to battle Azog will not only show Azog completely missing but, none of his fellow Orcs will be there either. It will be a completely empty field. To make sure this doesn't happen, the entire cutscene must be viewed.
Plot hole: Mario is arrested in the beginning of the game after Shadow Mario frames him for the evil paint. But before he is taken into custody, he gets his Super Water back pack called F.L.U.D.D. It is a high pressure water apparatus and a potential weapon. Yet at Mario's trial, and when he's in jail, he still has F.L.U.D.D on his back. The authorities would have taken such a device from him in this situation. Even in a fantasy world such as this, it does not make sense for them to let him keep the artificially intelligent water cannon with him during his trial, much less in jail.
Bug: When attacking people in a restaurant, some of them that are sitting will slump over and 'die' with their heads on the table. Yet they are still alive in the game. But you can't lock on to them. You can't kill or hurt them ether. Blood splats, but nothing else. Punching, using melee weapons, shooting, using the chain saw, and even throwing grenades of other uses of explosives doesn't do a thing to them but splatter a little blood. Yet this supposedly 'dead' person will still talk to you if you bump them. Sometimes they'll still do the random compliment or insult and you can still have CJ respond to them.
Bug: After about 10 minutes of gameplay, if you leave an area of the school and try to head to another, the screen will go black and the loading screen which shows a bubbling cauldron will appear. Unfortunately, the loading screen will not vanish but will remain. The only way to progress further if this bug occurs, is to reset the game console that this game is experiencing the glitch.
Bug: After the S.S. Anne is gone, go to the guard that says that the ship is gone. After facing him, keep pressing right and then quickly push the START button. Save and reset. If everything's OK, you should continue facing right. Select a Pokémon that knows SURF and use this move. Instead of surfing to the right, you'll surf ON the guard! Press down twice, and you'll enter the S.S. Anne again.
Continuity mistake: When the player is asked to choose between joining the Na'vi or the RDA after discovering that Harper is the mole, if the player chooses to stay with the RDA, then the player remains human throughout the rest of the game. One of the players missions will then be to kill Tan Jala, in which the player is of course successful. Near the end of the game the player then meets with a Na'vi leader who gives the player a choice to either remain with the RDA, or switch sides and help the Na'vi. If the player decides to switch sides and join with the Na'vi, after the RDA attack on the Well of Souls is repulsed, an Ikran appears with Tan Jala riding it.
Other mistake: On the thrill rides tab, find the ride: Top Spin. In the description of it, they spell heels wrong. They spell it heals.
Bug: If you drop paintbrushes out of your inventory, they float and are able to carry you on top of them, which you can do over and over to get really high on top of something.
Other mistake: The UK English instruction manual refers to Beedle as 'Terry', even though he is called Beedle in the game.
Other mistake: Even though premium cards are supposed to be unreloadable without using certain item cards, if a premium card is put second or third in a sleight, it can be reloaded normally.
Bug: If you fall in the water, your hat is temporarily removed, and when you go back to the surface, you have it on again. Well, if you get out of the water, and make Indy fall to the water just in the moment when he's putting his hat back on, it'll fall in the water and you can play the level with no hat.
Bug: There are certain parts of the game where you can play with the camera. In one of them, you can see through the Merchant's insides and you can see he's truly infected with Las Plagas! Watching him like this is really hilarious.
Plot hole: Cleaning out the Bureau: At the garment factory, Michael arrives, agent Dave Norton arrives and later in the scene, agent Steve Haines arrives at the building, walks up the stairwell and says hello to the others. Apparently, the plot has completely forgotten that Steve had shot himself in the leg in the mission "Monkey Business" a few missions prior, to make himself appear as a double agent - he is walking around completely fine in this mission as if nothing happened.
Character mistake: During the last class trial (06), Kyoko recapping the vitals of the victim gets them wrong, saying she was 5'6" instead of the correct 5'7" as written everywhere else. Nobody corrects her (and the exact vitals are an important part of the trial, and the mistake happens exactly when they come into play). A wrong number slipped in the script.
Bug: This glitch has been fixed in later versions of the game, but still works in the original NES version. When fighting the Yellow Devil, select your Elecbeam and fire it at the enemy's eye. As soon as you fire, start rapidly mashing the Select button over and over again as fast as you can till it hits. If done fast enough, the beam will instantly kill Yellow Devil in one hit.
Continuity mistake: In the game's final cut-scene, even if you had the M4, Niko will be armed with an AK-47.