1) Last summer I was working on experimental flood forecasting system for one big country. That day I managed to finish new version of web interface just in night before deadline and uploaded server-side scripts and model, written in fortran, to main server and client-side to webhosting (pretty silly, but that's not me who makes rules). After setting things up I realized that now client and server can't understand each other. Totally. Every single query. Setting my server as main not changed anything. Everything works fine on my testing system, but on servers of research center scripts just goes crazy and reporting about invalid queries.
The problem was in little hosting-side script, that was proxing requests. On my testing system all worked clean, but that server messed up json data, adding some punctuation to it.
Form that day I do not trust any software, which wasn't configured by me =\
2) Once I wrote CMS system. It was lacking of admin instruments, but because all of my team were skillful coders and community wasn't very big, that was not big problem. So, one day I was changing user's password's hash directly in database by UPDATE request and forgot WHERE part. That cleared passwords of all users. Last backup was about two weeks ago.
All old users was recovered from backup, but several dozens of new was missing. And, I hacked code so it will during login write down user's password's hash if there is no password in database. Silently.
No one ever noticed = D