I finally managed to run into the bug again, although I still don't know what causes it. Loading in the save file will get you right before Fuuka's arena. Going in, you will see that there are two of her.
I loaded in the save file a bunch of times and always got this result, EXCEPT when I did the following: I aggrevated the Fuuka on the bottom then immediately quit to the main menu. I loaded in the same save file as before, but when I entered the arena, it had a diffent layout. More strangely, instead of there being two Fuuka's, there was one real one and an impostor.
This also seemed to be reliably reoccurring. Quitting the game entirely and coming back to load in the save code once again would result in two real Fuukas being present.
Save file (will expire in 6 days): https://filebin.net/6lrq62wyizzp51nl