Close and re-open the game, when you get to the title screen with Rayquaza and the protagonist, press F5. It'll disable some graphics. Continue. If going through Continue gives you the same or stops you at the same point, start a new game doing the same thing (F5 at title screen). That should fix it. You can re-enable the pretty graphics after you get through that part. Maybe. I haven't done it.
Wait a bit for a new update he pushed out that should post soon. Version 1.11.0 was where that issue wasn't happening for me anymore. But he tried to fix another issue that he pushed out after 1.11.0 about a fatal error bug, so in case that may happen to you in the future, just get that new update instead.