Well... I once accidentally deleted a classmates entire assignment. Basically we were working together on one and we had the code in Github, I had named the repo after the module code.
He was having some weird git issues and I thought it would be easier to just delete and re-clone on his machine. You can probably see where this is going.

Me: rm -rf <DIR NAME> Enter
Him: wait, which folder did you just delete

Turns out he had the repo cloned inside another directory with the EXACT SAME NAME, which also contained his previous assignment, the only copy of it in the entire universe (it was a group project and they did it all on his laptop with no source control, which i found hilarious).
It wasnt so bad since that assignment was already submitted and graded, but a bit of a fail on both our parts.