* AmericansHateTingle: Manaphy gets disliked by Many American fans, due to it having tantrums without May so often, that it constantly comes off as whiny, But In Japan? It has beaten fan favorites like Celebi, Jirachi, Shaymin, and Victini in Pixiv's (Japan Only) Popularity Poll.
* BaseBreaker: May and Manaphy is either seen as an adorable relationship or a rip-off to Misty and Togepi.
* BigLippedAlligatorMoment: Team Rocket capturing [[OlympusMons Rayquaza]].
* ContestedSequel: If this movie didn't have it hard enough as it is, it had the misfortune of following up ''Lucario And The Mystery of Mew'', widely considered a SurprisinglyImprovedSequel and among ''the best'' of the Pokemon films. To say ''Temple Of the Sea'' had pretty lofty expectations to follow is putting it ''very'' mildly.
* EnsembleDarkhorse: Manaphy has only been around in one movie, but gets a lot of Fanart, and {{Youtube}} videos.
** Lizabeth can count, too.
* 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 saying "Hello"...until 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. And even if it could keep them alive, had Ash failed, they'd be stranded in deep waters in a claustrophobic tank and no one knowing their location]].
** In a similar note, [[spoiler:where are Ash's Pokemon (save Pikachu and Corphish) during the entire ordeal? If Ash died during the sinking, either of the two available options could be horrible to an extent: a) if they were staying in the Blue Lagoon, then they would the next day wake up and realize their trainer is gone, or b) they were with Ash the whole time; sure Swellow, Sceptile and Aipom could have jumped out of their Pokeballs to save Ash, but how about ''Donphan''?]]
* 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 or Enviously mentions that ''he'' wanted to hatch Manaphy with his own hands. Is this guy expecting parenthood or something?
* TheyCopiedItSoItSucks: A lot of Western viewers accused this film's plot for being a blatant ripoff of Misty and Togepi.
* ToughActToFollow: This movie's predecessor is ''Anime/PokemonLucarioAndTheMysteryOfMew''. Not exactly an easy bar to reach.
* 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.