Storyline's Sudowoodo bugged (?)

[Vanhven]

So I faced the Sudowoodo that wakes up with the squirt bottle (Johto, Route 36 or 37) and with a bit of effort I captured it and since it was level 25, higher than most of my other pokemons at that point, I decided to have it in my party as a reserve. Later on in a fight with a trainer, my leading poke died and when I tried to take this one out, it sent out another one, I didn't think much of it at the time because I thought I missclicked it. In a later fight Sudowoodo was my second option again, only that this time again, Cyndaquil went out again even though I clicked on Sudo. When Cynda died, I couldn't get Sudo out, but I was also unable to do anything else, other than closing the game.

 

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Any help is appreciated.

 

Edit: Seems that after a game restart (and a long queue) it fixed itself.