Several Pokémon cry flubs occur in "Pikachu's Rescue Adventure". Most notably, a Poliwhirl shouts "Poliwrath" and a Pidgey shrieks "Fearow".
Melody refers to Misty by name before Misty has even introduced herself.
Celebrity Voice Actor: In the original Japanese version, Lawrence III/Jirarudian is voiced by veteran actor Takeshi Kaga and Slowking/Yadoking is voiced by comedian Masatoshi Hamada. (Hamada being known best, overseas in the United States by Japanese culture enthusiasts, in the late 2000s, 2010s, and now the 2020s, for Gaki no Tsukai ya Arahende).
The ending theme of the Japanese version, tot ei moi by Namie Amuro, was thrown into the film against Takeshi Shudō's wishes, replacing a song originally written for the end credits based on the flute melody played by Melody (Fleura in the Japanese version). Even a decade after the film's release, the late writer expressed disgust over this change on his blog, which you can read a translation of here.
A scene got cut when it was dubbed: Basically, it had Tracey Sketchit deduce that the combination of water, electricity, and fire on the cages would cause an explosion before knocking Misty and Ash down seconds before the detonation, giving some redemption to his character (although some insist that the explosion was caused by Togepi because it was wagging its arms a few seconds before the explosion beforehand). The reason it was cut was because 4Kids feared that Tracey's explanation would have probably been used by the audience to create an actual explosive, though the line still appears in the novelisation and the ani-manga.
Also, because of religious matters, the three legendary birds (and Lugia) are referred to as Guardians, Beasts, and Titans instead of Gods (which was their original title). Averted however in the Finnish dub, where the legendary birds are referred as Gods.
The Red Stapler: Lugia was created specifically for this movie, and was added to Pokémon Gold and Silver solely because of its popularity among filmgoers. This explains why Ho-Oh was the only new major Legendary Pokémon in Gen II outside of the legendary beasts for much of its development, as well as why Lugia in the games is depicted as being the master of the legendary birds, which are from a completely different generation and aren't otherwise related to Lugia in any visible way.
Screwed by the Lawyers: In 2017, "Weird Al" Yankovic wanted to include his song "Polkamon" on his career-spanning boxset Squeeze Box, but Nintendo refused because they didn't want anyone capitalizing off of Pokémon GO.
This movie was originally going to compete with Disney's Recess: School's Out in July 2000 (Remember that WB and Disney have been competitors for a long time, and the One Saturday Morning vs. Kids' WB! war was being won by Disney at the time). Knowing about how big their competitor was, Disney decided to hold Recess off until February 2001. Though if both movies were released at the same time (looking at both box office numbers and reception from when both movies were released), Pokémon would have had better box office numbers, while Recess: School's Out would have more critical acclaim.
Trailers depict a few cut scenes. There's an unknown scene of Ash on a boat. There's also a scene of Ash jumping off a cliff to save Pikachu and then Ash's friends reacting to Ash jumping off the cliff (with Misty missing her jacket and crying).
According to Takeshi Shudō, his first draft for the movie did not feature Ash or any of the supporting characters from the anime. It was only at the urging of the higher-ups that he added them in later drafts of the script.
Shudō originally envisioned Pokémon X, the Pokémon that eventually became Lugia, as both a film-exclusive character and female, conceptualizing it as a maternal guardian of the sea. He did not contribute to the design of Lugia nor its name and was surprised to see Lugia included in Pokémon Gold and Silver and vehemently protested the decision to cast a male VA in the role, later regretting that he didn't lobby hard enough to preserve his original vision.
Word of God: The film's screenwriter established that Lawrence III (Jirarudan in the Japanese) isn't evil, comparing him to Don Quixote.
Misc.
Herman Cain infamously quoted the ending song of the movie The Power of One to close his election bid, attributing it to "a poet". Before, he thought they were the lyrics to the closing song of the 2000 Sydney Olympics. The Daily Show took notice of this.
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