Plot hole: If you use a Pokedoll against the Marowak Ghost in the Pokemon Tower, you can actually skip the battle and progress through the game, without ever getting the Silph Scope. This make no sense, you skip a large portion of the game this way. Just as an example, after skipping the Ghost, you fight Jesse and James with evolved Pokemon, but if you go to get the Silph Scope after this, they will be there, with unevolved Pokemon.
Plot hole: On The Skeld, ejection should be impossible without killing the entire crew. There is no airlock, meaning that as soon as the door opens to eject the potential imposter, everyone in the vicinity will be sucked out, as well as the air. Everyone would end up suffocating, and the garbage chute is too small to be used as an airlock.
Suggested correction: There's an airlock in Storage, and doors at the entrance to every room.
Then shouldn't loads of trash be ejected with them?
Plot hole: If you successfully go through all the red path on the Lylat System map and reach Venom, the Cyborg Star Wolf team still appears before you can fight Andross. They talk about your previous fight with them, and show their cyborg parts from injuries of crashing when you fight them and win on the third level on the blue path. But going all red path, this is the first time you meet them. So they are injured from you, but never fought you.
Plot hole: According to the Lore, Purple Guy hid in a Spring Bonnie suit to lure the kids into the room he would kill them in. This is a continuity mistake as well as a plot hole because the plausibility of the disguise is highly diminished when the Phone Guy tells you that the suits kill people when they get stuffed into them on Night 1.
Plot hole: When you enter Petalburg Gym for the first time, Wally enters and is given a Zigzagoon as a lend. Then, you have to follow him and watch him catch a Pokemon. The Zigzagoon is at level 7, so it should have Tackle, Growl, and Tail Whip. However, it does not have tail whip, which it has to learn at level 6. Also the Ralts that Wally's catching is level 5 and all ralts are level 4 in the wild.
Plot hole: In the "Blue Shadow Virus" level, when the clone trooper gets shot by Doctor Vindi in the clip, he reveals it to be a sticker. But the shot went right through his body, so there should have been a hole in his back. When he walks away, there are no holes, and nobody took a sticker off his back.
Plot hole: Reptile, in his chapter, says that he will distract the Outworld forces while being invisible. However, when the distraction happens, we get to see Reptile running on roofs...while not being invisible. And this impacts the plot because General Shao sees him and identifies him.
Plot hole: Pyscho says that he will provide support in the 2nd level, but there is no support at all.
Plot hole: The main character finds the dead journalist at the beginning of the movie, walks back to town using the main road, and when he gets there not only have the police found the cadaver already, but the barman knows all about it, including the outcome of the questioning of the witness. Stellar police work and mad gossiping skills, all without the police cars passing by the unsuspecting Thad and arresting him.
Plot hole: When Shoji gives himself up to the authorities at the end of mission 9, Aoki thanks to the Senpuji Industries lies to the inspector saying that he was a test pilot, but that does not solve the not marginal issue that the playing character comes from another dimension and has no ID. The inspector is a stickler for the rules but in all the hours of interrogation apparently the subject of their identity never came up.