* 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.''
* 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.
* 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.]]