Goofs

Melody calls Misty by her name before the two are ever introduced. It's been suggested this was because Misty is a famous gym owner and Pokemon master, though Melody doesn't seem to treat her as someone famous, and in fact another correspondent says she is not well known.

During the scene where Ash and Team Rocket are riding in the Air Boat to Ice Island through the tunnels, Jessie's characteristic pink hair changes to deep purple when they emerge from the tunnel into the small area with the third treasure. When they escape, and Team Rocket jumps onto Lugia's side Jessie's hair is pink again, and her purple hair is never explained. Frozen, perhaps?

When Lugia speaks for the first time, during the conversation he has with Ash in one shot his wings are flapping, in the next shot they are still.

Misty and Melody are the same height when they shake hands. Throughout the film, Melody was the same relative height as Ash, and Misty is several inches taller than Ash.

Melody calls Misty by her name before the two are even introduced. However, in the Pokemon world, gym leaders are known as celebrities. Since Misty was a leader, it isn't unlikely that Melody would know her name.

While most Pokémon are only able to say their own name, in the short "Pikachu's Rescue Adventure" that precedes the feature, a character is seen bouncing around and saying "Poliwrath." While some think that character looks like a Poliwhirl, it is indeed a Poliwrath - only the eyes of the two monsters differ.

Near the end of the film before Melody plays Lugia's song, the song starts playing before she puts the shell/flute in her mouth.

When Ash places the third treasure in the shrine we hear the "knocking" sound of it touching the pedestal before he places it there.

At the end of the film when Delia says "And remember, everyday you're my hero" and when Ash replies "Thanks, Mom." their lips are unsynchronized.

Ekans is seen swimming but Ekans cant swim.