Domino's Epic Fail, accidentally due to Jessie and James mopping the floor under her orders. The two of them don't miss the irony, and are quite pleased with the results.
Also, Jessie and Jame's pledge to help the clone Pokémon, telling them they'll go anywhere they lead them to. Immediately cut to the next scene, with the clone Pokémon locking the two of them in a prison cell.
"Finally! A man with intelligence, intensity and ruggedly attractive stubble cares about me passionately!"
James seizing Pikachu with electricity-absorbing wire. Specifically, the way he announces it as if he was sending out a Pokémon.
Luna calls the Team Rocket trio "careless and reckless" after they take off in the storm with Pikachu. Domino responds with a deadpan "You forgot to mention brainless." Even better, this happens before she formally reveals herself to be Team Rocket and while she's still pretending to be an airhead (but after the audience is clued in), yet nobody notices the sudden change in demeanor, making the whole thing a hilarious extra bit of Dramatic Irony.
Mewtwo in the Japanese version when confronted about saving a bus full of humans. While the English version has him coldly dismiss the notion that he might be growing a soft spot for humans, here, his reaction is a Tsundere-like denial.
"Do you think I'm a Pokémon capable of being that kind to humans? Me? Mewtwo? Don't be ridiculous."