Oh I'm sure I could think of a lot of these! My most recent one was when I wanted to replace a single DLL on our production server (Joe made a bug fix in the MySQL data layer of Form Wizard Pro). Being a cautious person and wanting to make the change as quickly and seamlessly as possible, I made a quick backup copy of the DLL file with Windows Explorer, then overwrote the original DLL with the new one.
BAM! Server starts spitting out 500 errors.
Uh oh, better copy the backup file over the top of the original. Whew, everything is working again. I go through the system log and come to find out that IIS is tied in so closely with the file system that when I made that backup copy while the site was up, it got incorporated as part of the running code, and the server was confused when I overwrote the original. So since I had an offline backup of the DLL from the previous night in case I needed it, I went ahead an just overwrote the original DLL and everything worked perfectly fine. Lesson learned!