They all look the same except totodile's pokeball.
Its a cartoon. Maybe they just memorize the spot the left the pokeball. Other than that there is no way to tell the designers just made it that way so battles and other events can go smoothly.
Thats because they arranged their Pokemons in order something like how we do it in the game where we choose who goes outs 1st
The anime is a not very detailed show that doesn't lend itself to logic, like many shows. In other words, it is a show for kids that doesn't always make sense. The Poke'mon Company must not have thought it a relevant detail nesesary to the show.
In the anime, the basic Poké Ball is the most commonly used of all varieties, with other varieties appearing either very few times or not at all. A vast majority of Pokémon are shown to be stored in regular Poké Balls, to the point that large collections of Poké Balls can be seen with no variation among them.
So it is just the anime.All sorts of things can happen.Maybe for checking they open the pokeball and check what pokemn is there and the Pokemon return baack to the pokeball.It is just the anime like I told you.