Alice is dumber than Ash
When Palkia and Dialga are fighting it out, Alice - who is hundreds of feet away - screams out, "Stop fighting right now!" Did she really think they could hear her? Did she think they'd actually stop?! I could picture Palkia saying, "You know Dialga, we should really stop fighting right now. Despite the massive damage we've been causing and the massive noise that comes with it, I heard this little girl say we should stop. What do you say buddy?"

Pokemon = Macross
So the big human contribution to this movie is that they stop all the carnage with a magic song. This plot device was ridiculous and stupid in Macross. It's still ridiculous and stupid more than 20 years later.

Inappropriate movie title
If anything, this movie should have been called The Fall of Darkrai. He pretty much gets his butt kicked in the movie.

Ash Ketchum is still stupid, part II
When Ash uses Pikachu to power up the magical music machine to play the magical song that saves the day, he commands his electric rodent to zap it with a Thunderbolt attack. Wouldn't Thunder have been more appropriate? There are no accuracy issues involved with a stationary target and it's a more potent attack.

Finishing school saves all
You know, Darkrai would have far fewer problems if it attended finishing school. Its unkempt and menacing looks coupled with its grating voice make it a scary Pokemon. If it looked and spoke in a friendlier fashion then far fewer people would assume it's the bad guy.