According to Japanese airing dates, the movie premiered in between "Reunion Battles in Nimbasa" and "Cilan Versus Trip, Ash Versus Georgia".
So I guess the heroes just took a break from the tournament to go get into wacky antics with Zekrom/Reshiram. Serebii lists it before the Nimbasa tournament, though.
Since you're already in the middle, I guess you might as well watch it after the conclusion of this tournament.
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http://i50.tinypic.com/23qx00.jpg
"First time I got punched in the face, I was like "oh no", then I was like "this is a story"."