The fact that the three Legendary Birds can overpower Lugia.
Also, Misty saving Ash from drowning and Melody playing the song that helps save the day.
A minor one, but the huge converging energy beam that Lugia fires off toward the end, which is most likely its signature move Aeroblast. The first shot damn near bisects Lawrence's massive airship, and the second shot knocks the Legendary Bird Trio for a loop even though it doesn't directly hit any of them; just passing near them for an instant is enough.
Ash gets a few in the movie too. The way to the last island is blocked by fighting birds of doom, icebergs, and a snowstorm? He builds a DOGSLED and has his team pull him over!
Zapdos and Moltres attack Ash on his makeshift sledge. Pikachu and Charizard counter with their own Thunderbolt and Flamethrower, respectively. Pikachu and Charizard WIN!
Also, Charizard nonchalantly dodges as Articuno tries to divebomb him.