I have this same issue coming up. The thing is once this starts popping up all the girls say to busy to interact with them. Any way to skip this issue or something?
I am playing the latest version, new save, and I'm seeing these too. They appear to occur after school hours while inside school property. I assumed they were related to the after-school meeting you can eventually have with Mitsuko, Aiko, and Saiko but I haven't gotten there yet and hadn't noticed any other unintended behavior so I've been ignoring it