>>49916549The second movie implied "Legendary" pokemon have a protected status in the eyes of the law since they are tied to the natural stability of the world.
A pokeball automatically registers the caught pokemon under the name of the trainer. (That's why when you have more than 6 pokemon, they get automatically Teleported away.) There is a monitoring system tied to pokeballs and pokecenters.
If you were to catch a legendary pokemon with a pokeball, the authorities would probably make you release it.