There are two instances of unlocalized Japanese text in the English version of Shin Megami Tensei IV: Apocalypse, and Atlus is very sorry about it.
In a blog post on Atlus' website, the developer explains that the Japanese text springs up during a boss battle near the end of the 3DS game. It wasn't spotted by its QA team, Atlus explains, because the QA team had never encountered those particular circumstances during that particular battle.
"The two instances of Japanese text left in the game happen during a boss battle near the end of the game", wrote Atlus. "As you may know, SMTIV:A has partners that are permanently with you throughout the game, and you can select the partner based on what abilities they have that complement your play style. (No more worrying about a randomly chosen Walter casting Agi on demons that resist fire. WALTEERRRRRR!)