Plot hole: Scar tells the pack he didn't make it to the gorge in time to help Mufasa. However Zazu was with them at at the gorge. He could have easily told Sarabi or any of the other lions on the numerous times he spoke with them, exposing Scar.
Suggested correction: Actually, Zazu wouldn't honestly say that Scar was lying; he left Scar at the gorge, but for all he knows, when Scar talks about not getting to the gorge in time, Scar could just mean that he couldn't find a safe path into the gorge to help Mufasa and Simba escape.
Suggested correction: Zazu wasn't with them when Scar said so. He was with Rafiki. He couldn't have heard what Scar was saying.
Suggested correction: But it wouldn't have confirmed that he killed Mufasa.
It would prove that Scar (who had the most to gain from Mufasa and Simba's deaths) was lying about the circumstances surrounding their deaths. But no-one brings it up.
It would prove Scar is lying about the events of Mufasa's (and Simba's presumed) death, and given Scar gained the most from it, the other animals should be extremely suspicious of him.
Plot hole: After Pikachu and Mewtwo begin falling down, Tim is suddenly on the ground in a matter of seconds, with little to no time to arrive there. There are multiple stairs, and he does not have any Pokémon to help him get down. He couldn't have gotten to the ground that fast.
Plot hole: SPOILER ALERT! During the final fight, Joey kills Frank and she reverts back to human form. Abigail tells her she's fine, because Frank was the one who turned her. However, when Frank kills Lambert he does not revert back to human form, even though Lambert was the one who turned him.
Suggested correction: Because it was too late for Frank, who had already turned, Joey hadn't.
If that were the case, then why would Abigail bother explaining to Joey why she reverted back to human form?