I actually had a backup save of this file in my recycle bin when I was swapping to my original, so I was able to revert it back to before I entered Grand Dream City and restart that whole part; it seems I was rushing through everything too quickly. Maybe the speed up/esc to skip dialogue needs some fine tuning to prevent issues such as these? I've noticed similar issues such as the one Layle reported, when skipping through scenes quickly, which I tend to do if I soft-reset and have already read/watched scenes/
I've noticed this happens if you have the scene sped up/hold esc to skip the dialogue as she acted normal in my first playthrough at normal speed then I did it in my second playthrough and she ended up there.