Encountered another very similar error when soft resetting during Mercenary Yior battle. The reason for the reset was because when I switched to Pikachu, after my Swampert hit red health, the issue of the UI disappearing still happened. I could not do anything and my only option was to soft reset, but that threw this error.
I got this error in v. 2.4.0.1 when trying to battle Mercenary Yior, trying to battle her again, will update if a restart fixed this error.
Edit: In my original run when I received this error, I actually clipped through the strength rocks under the bridge and never received the HM for Strength from the grunt. Upon reloading I couldn't clip through the strength rocks and did the proper order of battling the Grunt and getting HM04. Upon beating Larry and Sherry, after that I was able to successfully battle Mercenary Yior. 
