* BigLippedAlligatorMoment: Team Rocket capturing [[OlympusMons Rayquaza]].
* CrowningMomentOfHeartWarming: May and Manaphy goodbye in the end.
* FridgeHorror: When Max is looking at one of the water-globes with the Pokemon in them, a Gorebyss pokes out of the water and startles him. One might assume it was just sayinh "Hello"... untill you realize that Gorebyss is a ''vamparitic parasitoid'' that sucks its victims dry and kills them. It wasn't greeting him, ''it was trying to feed on him.''
*** Well, it was a tamed Gorebyss. It probably gets fed by its owners, and they're right nearby if it tries anything, so...
** Ash [[spoiler:''stuffing May, Manaphy, and Pikachu in a very small tank'' as he goes off to restore the power to the temple alone. There was no visible air tank on that thing and somehow the three of them taking all the air didn't suffocate them]].
* JustHereForGodzilla: Some watched it for Kyogre, who only shows up at the end.
* {{Narm}}: Manaphy directing the Pokémon in the final battle. AChildShallLeadThem, I know, but still...the ''voice''.
* MostAnnoyingSound: Manaphy's shrill voice and cry, including the scene where it cried or threw a tantrum/meltdown over May's absence before it uses Heart Swap.
* OneSceneWonder
** Ash's Hoenn Pokémon, except [[EnsembleDarkhorse Corphish]], only appear for a few minutes. And it's in those few minutes that we get to see [[{{Badass}} Sceptile]] in his '''only''' movie appearance.
** Kyogre shows up at the end for a few minutes tops [[TrailersAlwaysLie despite being advertised as being the token Legendary of the movie.]]
* {{Squick}}: Phantom heartbreakingly mentions that ''he'' wanted to hatch Manaphy with his own hands. Is the guy expecting parenthood or something?
* TearJerker: May and Manaphy's goodbye.
* TheScrappy: If you don't like Manaphy and its shrill voice and cry, you can [[RevengeFic just imagine it to let it burn in hell.]]
* ViewerGenderConfusion: Though its higher voice and pony tail-like antennae may make Manaphy seem like a female, its gender is never officially mentioned, so its real gender is unknown. It's maybe leaning more towards male since it's named the "''Prince'' of the Sea" a countless number of times. [[DudeLooksLikeALady However, it still looks like it should be female, though.]]