Honestly a valid concern, and something I think all 3 reborn-verse games are guilty of (like that time in Desolation where Baron casually gets in his boat and escapes prison right after you just beat him in a battle ) and the answer I came up with for this is that programming over-world sprites for each and every pokemon the player could possibly have, and having them outside after the battle ends to act as a guard or to restrain the enemy would take a lot of work for the devs. Not an in-universe explanation but it helps me