Asspull: Darkrai's sudden resurrection at the end may come off as rather sudden, and a bit unexplained. note Most of the town itself was disintegrated into dimensional nothingness, then reverted back to normal; it's possible the same was done with Darkrai.
The two songs during the end credits, "Living in the Shadow" and "I'll Always Remember You."
Darkrai's leitmotif. A chilling bell gives way to strings and a creepy organ downbeat.
Broken Base: Some people think this movie is one of or the best movie in the franchise, most people find it So Okay, It's Average, while a few people think it's one of the worst Pokemon movies.
Creepy Awesome: Darkrai, a living shadow that fought against two deity Pokémon. Even better was that he was only acting scary to prevent the deities from ruining Alamos Town's garden, which was for everyone.
Critical Research Failure: The only Shellos that appear in the movie are of the East Sea variety, although Alamos Town is actually on the west side of Mt. Coronet.
Designated Villain: Dialga has as much culpability in what goes wrong as Palkia does, and yet just Palkia is deemed the villain by the movie.
Fan-Preferred Couple: Darkrai/Alice since the former risked his life to save the latter multiple times, while the latter felt worried whenever the former was hurt. You'd be surprised to see how many fans ship them instead of the Official Couple Tonio/Alice.
Genius Bonus: The Oración piece drawn at the back of the photograph of Gody and Alice on a bench, if played in the treble clef, is the same as the Oración actually played during the movie, albeit only the melody line.
Iron Woobie: Darkrai, who never meant any harm, was cared for by Alicia, and went on to eventually save Alice's life, was still oppressed and antagonized by the people of Alamos Town.
Seeing Darkrai himself get disintegrated, bit by bit.
A nightmare within a nightmare: when Ash was put to sleep by Darkrai's Dark Void, he sees a really menacing projection of Palkia.
Watching Alamos Town slowly disappear into another dimension by Palkia.
Paranoia Fuel: You see the vast fog over your town? That's no ordinary fog. Behind that fog isn't clear blue skies, but a whole different dimension that some invisible being has sent you in. Oh, and by the way? Your loved ones who are asleep will never wake up and are suffering from never ending nightmares. And all because their captor Darkrai is trying to stop a dangerous battle between the Pokemon of time and space.
The idea of Darkrai being seen as the villain before The Reveal that he isn't is half-baked in execution, largely due to the fact that the movie itself barely attempts to suggest that Darkrai may truly be evil. Instead, characters justify his seemingly malevolent actions at almost every turn and downplay his ominousness, denying the audience much reason to assume he's evil at all before his true nature is shown.
The final fight between Dialga and Palkia is mired by it only coming into play at the end and the stakes only affecting the human characters, whom are far removed for the battle. At least one critic has compared the climax to that of Pokémon 3, and how it falters by comparison.
Viewer Gender Confusion: Although it has no gender in the main games and is a male in Mystery Dungeon, more than a few viewers thought that Palkia was female. This may be due to the fact that Palkia has wide hips and a low waist-hip ratio, has stiletto clawed feet, shares the same roar as the female Boga, and is freakin' pink whereas Dialga is blue.