Once I had to track down an issue where very rarely, with no discernible pattern the web app would produce garbled PDFs. Turned out this happened when an admin account remotely connected to the app server, which caused a reset of default screen resolution, which messed up the PDF library that relied on a specific resolution (it was HTML-to-PDF conversion). Happened rarely and randomly because there were multiple web servers and they were occasionally restarted which would fix the problem until next time.
Another fun problem I dealt with was when I was moving my employer's codebase from Subversion to Mercurial version control ages ago. Everything looked good, except a directory named CVS (after the pharmacy, a customer) was missing. Was banging my head on the table before realizing that the default .hgignore file instructed Mercurial to ignore all contents of .*/CVS (another old version control system).