The latest Pocket Monsters movie debuted in Japanese theaters on July 14th, 2012. The 15th movie Kyurem VS the Sacred Swordsman Keldeo (キュレムVS聖剣士ケルディオ ) and its short Meloetta's Sparkling Recital (メロエッタのキラキラリサイタル) were unable to take advantage of a weak movie debut week compared to previous years and ended up in second place. It made 753,760,100 yen for the three day weekend period.


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.

Source: http://eiga.com/ranking/

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.

At least it wasn't Harry Potter this time, otherwise I would've headdesked for 2 hours straight.