It is available, but only if you have Hoopa
>In Pokémon Omega Ruby and Alpha Sapphire, the Prison Bottle can be obtained >through having Hoopa in the party and entering a Poké Mart. A new clerk will show >up near the counter at the far left side. If the player interacts with this clerk, the game >transitions to another view as the clerk tells the player a story.
>After his story, he will give the player the Prison Bottle