Loving all the updates!
I think right now the biggest issue is if any pokemon end up off outside the box and off screen they seem to lag the game a lot, I've had runs that could've lasted longer had this not happened and made the game so slow that I couldn't continue.
Pokemon being outside the box isn't really a problem and can actually be handy sometimes for cleaning up the board, but they should probably be deleted or ignored in some way once they're far off the screen.