Factual error: In "Pikachu and Pichu," when Pikachu and the Pichu brothers come to the big play structure thing, there are a bunch of Pokemon around, including a red-and-white, ball-shaped Pokemon called Voltorb. The dubbers for the English version made a very noticeable error here: instead of Voltorb saying "Voltorb," (almost all Pokemon say parts of their names when they speak) it says "Electrode," which is the name of a similar-looking, but different Pokemon. The two are both red and white, but the difference is that Voltorb has eyes on the red part of its body, while Electrode has eyes on the white part of its body.
Continuity mistake: In the third segment of the movie we see Davis, Yolei, Cody and their Digimon playing on the beach. In the wide shot when we see all of them playing we see that Davi's Digimon is in his "rookie" form, Veemon. When they show a closeup of him and Davis together, Veemon is now in his "in training" form DemiVeemon. Then they show them all playing again and he is now Veemon again.
Other mistake: Ginger is adamant that she will not approve any plan of escape that does not get all the chickens on the farm out and to freedom. The problem is, not one of her plans gets anywhere close, and it is not that they fail to liberate the whole farm - they are never planned that way. We see her trying to escape by herself three times. The mannequin of Mrs Tweedy would (had it worked) have allowed nine chickens to escape, the upturned feed tray just seven. Even the 'crate' appears to hold not more than thirty chickens - and there must be several hundred on the farm, at least.
Continuity mistake: After Spike chases Jean-Claude out of the church, the parents and their kids stand outside. Chuckie is in his father's arms holding his Wa-wa (teddy bear). They go back inside, where Kira gives Chuckie that same missing teddy bear.
Continuity mistake: When Kronk is disposing of the llama body, he runs down a very tall staircase. At the bottom, he runs into two peasants and leans up against the wall. The peasants pass him, walking toward the left side of the screen. Immediately after they disappear from the screen, the "camera" zooms out so you can see the entire palace. Now, the only place the peasants could have gone was up the staircase Kronk had just come down from, unless they wanted to fall off a cliff. If you look on the stairs, though, no one is there. The peasants couldn't have made it all the way up the extremely tall and steep staircase within seconds, so they just mysteriously disappeared.
Revealing mistake: When the Pterodactyl is flying around with the egg, its shadow isn't cast as she flies over the trees.
Continuity mistake: During the scene where Akima gets out of the shower, we see Cale going over some of the stuff she collected that's sitting on her table. On it there is a baseball and a picture frame that's lying flat on the table. Cale picks up the baseball, says something to Akima and puts the baseball back down on the table, where it rolls over the picture frame as if it was flat as the table.
Plot hole: There's no visible evidence that Team Rocket has taken away Ash, Misty, and Brock's Poké Balls when the gang was in the cage, so why don't the Trainers call out their Pokémon (Brock's Onix would've helped out very much) and escape the cage?
Deliberate mistake: You might be wondering where Terry suddenly comes up with Jolly Jack all of the sudden after escaping the lab. In the commentary, they say that the Joker, in his transmission to Terry in the lab, was supposed to be eating out of a candy jar with "Jolly Jack" on it, but couldn't have it due to time constraints.