We're going to have to say no to Milotic, sorry! And Togami winning is fine!

As far as the Pokeball question goes, due to the train being on high alert, things like that are going to be checked before boarding and asked to be deposited in a conveniently placed PC. With the current threat going on, they're not going to want someone to take something like a Wailord onboard in a Pokeball and then use it to derail the train after it leaves the station.