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.
Plot hole: In the PlayStation 2, GameCube and Xbox video game adaptations of Harry Potter and the Prisoner of Azkaban, Draco Malfoy uses the polyjuice potion to turn into Ron to trick Harry into following him into a trap while trying to find Sirius Black. Despite the fact that the Map never lies about identity, it still names Draco as Ron.
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.
Suggested correction: Maybe he quickly recovered? Sometimes injuries heal quickly.
Plot hole: Drake is supposed to be discovering lots of things in the game for the first time, yet every secret door or area he explores, there's always enemies there. If he's supposed to be the first one there, how can the enemies be there before him?
Plot hole: It's funny that Doc McCoy's special sniper ammunition for his Buntline can be found in various other locations even though he says in his tutorial that he crafts these bullets himself.
Plot hole: Even if you've acquired Piers's ship before visiting Garoh (a city populated by werewolves), when you first set sail in Piers's ship, Sheba will say, "We've already met werewolves."
Plot hole: When Umbride is about to use the Cruciatus curse to interrogate Harry towards the end of the story missions, Herminone says "Tell her. It's not worth another student dying." No students had died (not since Cedric Diggory anyway), were threatened with death or were in any kind of fatal situation yet. What is she on about?
Suggested correction: Exactly what she means. Cedric Diggory is dead so it's nothing worth Harry to die over.
Plot hole: When Tails is flying towards Prison Island for the first time, he spots Amy on the island surrounded by enemies after mistaking Shadow for Sonic. There is no explanation given for how Amy arrives on such a guarded and fortified island. When Sonic asks her later, she says that she hitched a ride with Tails in his plane, but she couldn't have, as Tails spotted her on the island as he was flying in.
Suggested correction: Amy was talking about how she made it inside the prison, not how she made it to the island. There being no explanation of how she made it to the island isn't really a plot hole either way. It's just something that is never explained.
Plot hole: Nick Fury is talking with The Silver Surfer after Magneto has been defeated. Nick asks for ideas on how they can save the Earth, and the Silver Surfer states that they need his board. Nick asks what Doctor Doom wants with it, Silver Surfer says something about Loki and the power cosmic. With almost no chance of saving Earth, Nick decides to put in an outside call and has Agent Hill call Mr. Fantastic and the Invisible Woman. The scene switches over to the Baxter Building where Magneto crashes through the roof and Agent Hill then calls them and says to them "This is Agent Hill from S.H.I.E.L.D. Director Fury is in urgent need of your assistance. Agent Coulson is on his way to pick up Magneto." There is no way Agent Hill, Agent Coulson, or even anyone who works at S.H.I.E.L.D. could have possibly known Magneto was going to crash through the Baxter Building roof. Magneto had only crashed through the roof a few seconds prior to the call and they had no idea the precise direction in which Magneto was falling in. Agent Hill established through the call that Coulson was already on his way over to the Baxter Building, so even if Agent Hill had seen Magneto on the floor through the call, there is still no way she could have gotten the word to Agent Coulson that Magneto was there anyway.
Plot hole: When Sonic and Tails land on the Egg Carrier, Tails reminds Sonic that they have to go look for Amy. But Sonic never told Tails that Amy was on the Egg Carrier, and Tails was not there to witness her kidnapping, so how could he have known?
Plot hole: In the mission 'Escort', Mobius 1 is well inside Stonehenge's engagement zone (As shown by the map during briefings), yet throughout the whole mission, the cannon doesn't fire, even though Mobius is also well above the kill zone altitude. (2000 feet).
Plot hole: Instead of going to the SS Anne, you can have a Pokemon with Cut traded to you. This makes no sense, you skip a part of the game by doing this. Also, if you advance in the game and then return to the SS Anne, Gary will appear there with weaker Pokemon than the ones he already has. Makes sense? No.
Suggested correction: You can't trade Pokemon with HM moves.
That only applies to later games.
Plot hole: In the levels 'Rebirth 1' and 'Rebirth 2' Wesker encounters Lisa Trevor and during their fight he calls her Lisa Trevor. This makes no sense because in Wesker's report 2 he says he never knew her name. Quote from Wesker's Report 2: "Even now, I still do not know who she was and why she was brought here".
Plot hole: In the level A Show of Force, Bond has to drive the Q-Bike. It seems that this bike came from nowhere, as it wasn't there the first time he went to the safe house, and 003 was already captured. No one could have put it there.
Plot hole: When Henry and Ellie are cornered in the launch tower during the 'Toppat Recruits' and 'Pardoned Pals' routes, the former goes back in time so that the soldiers that apprehended them were never recruited and therefore the main characters are no longer cornered in the present. However, this should simply cause different people to try to stop them, not an entire removal of the threat.
Plot hole: Level Five: After finishing the mission to defeat The Dirty Bubble atop the Sea Needle, the game completes, the Dirty Bubble is stopped and Bikini Bottom is saved from the little dirty bubbles infecting them. After saving the day, the game lets you go back to Bikini Bottom to finish off some other missions, but despite this the citizens are still infected by the little dirty bubbles and if you go back to the Sea Needle, the Dirty Bubble is still waiting there and reading to be battled again.
Plot hole: At Scorpion's bio, it was revealed that he was asked to join Shao Kahn's army, and apparently, Scorpion agreed until he discovered that Sub-Zero, who in the last game he had sworn to protect, was in Earthrealm, which was being invaded. It makes no sense as to why he would ever join Shao's forces after fighting against them in the previous game, and we aren't told if Shao made any kind of deal with him. An in-character Scorpion would have either resisted the invaders or stayed out of the conflict.
Plot hole: Brooklyn Mission 2: After Reed and Sue confront Ben, he smashes down a fence and takes off. Only on the other side of the fence are 3 members of the Yancy Street Gang. The fence even hits these three guys and Ben runs between them. Yet, despite the fact in the previous mission, Ben took out many of their fellow gang members, including their leader, they act like they don't even see Ben. They ignore him completely as he hits them with the fence and plows between then. And then they charge at Reed and Sue to attack, and they have never even seen Reed or Sue before, nor has any of their gang.
Plot hole: At the Ruins of Alph, when you solve your first stone puzzle, you fall down to the ruins, where there is a "strange presence". Now, you can encounter Unown, a Pokemon. After this, you tell the scientists nearby about them, and help them solve the puzzle. However, if you make it out of the Ruins without seeing any Pokemon, talk to the scientists and they still know about them, even though you haven't seen them.