Plot hole: Officer Jenny asks Ash what he knows about the "trio" when he tells her that the pirates are likely Team Rocket, but he hadn't said anything about there being three of them before that. And Jenny obviously didn't know anything about Team Rocket, either. (00:05:30)
Plot hole: After Ritchie tells Misty that he never talked to them through a phone, Misty could have put two and two together and realised that Ash was told to go somewhere by someone impersonating Ritchie and that he might be in serious danger. However, she does absolutely nothing to help Ash, she doesn't even inform Brock about it.
Plot hole: When Team Rocket decides that they're going to capture Dragonite after it's been worn out, they appear in the blimp above the battlefield no less than ten seconds after they were shown in the stands. There is just way too little time for them to have possibly gotten up there that fast, even allowing for anime physics. (00:14:30)
Plot hole: When Officer Jenny says why Captain Aidan needs to get Team Wartortle to the shot of the final fire, she says that Team Blastoise's path is blocked by a lorry, and Team Squirtle is not powerful enough for the fire. This does not make sense for the former as Team Blastoise later pushes the same lorry aside. (00:13:41)