Americans Hate Tingle: 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.
Base-Breaking Character: May and Manaphy is either seen as an adorable relationship or a rip-off to Misty and Togepi.
Contested Sequel: 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 Surprisingly Improved Sequel 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.
Fridge Horror: 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 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, 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?
Viewer Gender Confusion: 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.