There's also the chance of it happening when writing a script

Such as this classic:

https://github.com/MrMEEE/bumblebee-Old-and-abbandoned/commi...

Ten years prior to that, Apple had a similar bug in one of its installer scripts on OS X. I have a hard time finding much about it online now, because it happened at a time when OS X and the Internet were a lot less popular than today, but what I recall is that an unexpectedly customized installation directory (say with spaces or one level closer to "/" than the default) would cause the installer to delete a whole lot of things.

I once installed GGClient in C:/Program Files/ instead of any particular folder

so of course, I said "I'll just uninstall it from there and install it in the correct folder" and it proceeded to delete C:/Program Files/

There's also this one from Pool of Radiance's 2001 release:

http://www.rpgfan.com/news/2001/1416.html

Uninstall wipes out your Windows directory.

I still have nightmares from this buggy mess. To add insult to injury the shop didn't want to take the game back afterwards.

The one that I did only a few months ago was something like

    $ cp -r path/to/some/directory path/to/very/important/directory
    $ (run some commands to verify copy did what I wanted)
    $ rm -r path/to/some/directory path/to/very/important/directory

Of course, all I had meant to do was delete `path/to/some/directory`, but I just pressed 'up' in my history and switched `cp` to `rm`. Of course I hit Ctrl-C in an instant, but my FS was already hosed...