No, nothing of the sort happened to close the game.
The first time I encountered this, I was forced to close the game before saving, so I did essentially restart from scratch and that did not fix it. I can verify that the download was not corrupted either.
Like I said, I got past it by not resting my pokemon after, and because of that, losing the next scripted battle. This leads me to believe that it is in fact a bug in the game's logic.