This example comes from a long while ago, but is relevant still.
A game company released an expansion for their game and soon after that there were reports from players that their computers are not starting up any more. Feels unbelievable, but after few more hours it was apparent that in some cases the installer script deleted the windows boot.ini file. The company explained the issue later on here.
What am I referring to, is the fact that even though everything might be ok inside the files of your program, using file names that collapse with system files (or crucial dll’s) might have unexpected results. When developers are lazy and using common words (config, boot, system,etc) bad things might happen. This also applies to web systems, as people can guess your config file name and path and thus get your sql server password or something similarly private.