If I'm looking at this right, I'm using Dolphin 5.0-3627
And I've discovered it only needs me to force close Dolphin if I'm in fullscreen, if I'm in windowed then I can just spam click on the "Okay" on the error box and it'll just resume.
It also seems to do this after I select the final move on my second 'mon, on every turn starting from the second turn, and I get a large number of these dialogue boxes every time. I seemed to get less dialogue boxes when I had Eevee use bite though, when I was mostly using Iron Head, Zen Headbutt, and Fairy Wind before then.
