I was working on a file for half the day - making layers, groups and text styles. I had it all the way I wanted it, ready to add some translated text tomorrow. I saved and closed, not realizing that the original file I opened was a PDF that had be saved without Illustrator editing.
The result was that everything was collected into one layer with nested clipping paths, and all my carefully formatted text was broken apart. (a few random lines were even converted to outlines)
Yes, it's my fault for not saving as AI at the start of my edits, but a warning dialog upon closing would have been nice This file will lose layers, styles and other AI editing features once closed -- some text may become outlined