BRAVE HEARTS Umizaru (海猿) which debuted on July 13, 2012, a day before the Pocket Monsters movie, took top place for the weekend. The extra day of ticket sales could have been a large factor in the box office sales position.
Title: Re: Pocket Monsters Movie 15 Debuts 2nd at the Box Office
I don't know anything about that BRAVE HEARTS movie, but it looks like a pretty big one, so it's not really surprising it beat Pokémon.
Still, that's not really disappointing for Movie 15, this is far from being the first time it didn't debut 1st at the Box Office in Japan.