Abilities don't work in the anime like they do in the game.
It's not so much as Greninja having the ability 'battle bond' - abilities are very rarely used in the anime, apart from the occasional static, overgrow and the new mega launcher in Kalos anime.
It's more likely the ability doesn't exist in the anime at all - Ash's Greninja doesn't change form when it KO's a Pokemon, for example.
