Just fast travelled to route 9 with Kanon and Melia after leaving the hospital of hope (and having a chat with Damien) and get black-screened anytime I try to encounter a pokemon or initiate a trainer battle. Reverted to a couple previous older save files and was still having the issue there as well. Not sure why this is happening or what could have caused it, but it was happening prior to the cutscene mentioned above.
Game.rxdata
Edit: The cause of my issue seemed to be having Turbo Speed at 2.5x. Once I changed it to any of the other options, saved, then reloaded the game, I could battle fine.