Yes, I hit that yesterday while playing with my Sort CSS plugin. I was simply writing lots of stuff to the console to get a better idea of what was in the files and not making changes, but I was still prompted to save changes when I exited.
OK, I just looked through my code and commented out all the things I thought it could be. Still had the update needed. But, the first pass I missed one. After the display of the differences I have
Code:
self.boss.apply_container_update_to_gui()
That seems to be the trigger. Even if I don't actually make any changes, executing that line will mark the file as dirty and need a save. That's probably reasonable.