At one point when Ash and Dawn are escaping the Reverse World through a dimensional hole, Team Rocket comes running up wishing, too, to get out. However, after Jessie runs up and jumps, the hole disappears. Newton ends up catching her before she falls into the abyss, and the next scene shows Jessie's comically pained face.
Ash: What happened to all the confidence you had in Sky Forme?
Shaymin: I left it all up in the sky.
The face Giratina makes after realizing that it caught "substitute" Shaymin instead of the real one. Its face◊ is like, The hell!?
This line of dialogue:
(After eating one of Dawn's puffins)
Shaymin:Dawn you're wonderful. (Under its breath) Way nicer than Ash.
Ash (angered):Oh, yeah!
(Shaymin burps black smoke in his face.)
Ash: Ah! Why you little!''
The part where Ash didn't wash his hands during the beginning. It's a good example of Tastes Like Diabetes...
Newton's reaction whenever Shaymin calls him 'a weirdo'.
There's one moment where Ash and Dawn are commenting on Shaymin needing to leave... and based on everything that's happened to him, Ash is grateful for that. This ends up with Dawn stomping on his right foot.