Most of mine are variations of getting confused about what system / device is which:

• Had two magnetic HDDs connected as my root partitions in RAID-1. One of the drives started getting SATA errors (couldn't write), so I powered down and disconnected what I thought was the bad disk. Reboot, lots of errors from fsck on boot up, including lots about inodes getting connected to /lost+found. I should have realised at that point that it was a bad idea to rebuild the other good drive from that one. Instead, I ended up restoring from my (fortunately very recent!) backup.
• I once typed sudo pm-suspend on my laptop because I had an important presentation coming up, and wanted to keep my battery charged. I later noticed my laptop was running low on power (so rushed to find power to charge it), and also that I needed a file from home I'd forgotten to grab. Turns out I was actually in a ssh terminal connected to my home computer that I'd accidentally suspended! This sort of thing is so common that there is a package in some distros (e.g. Debian) called molly-guard specifically to prevent that - I highly recommend it and install it now.
• I also once thought I was sending a command to a local testing VM, while wiping a database directory for re-installation. Turns out, I typed it in the wrong terminal and sent it to a dev prod environment (i.e. actively used by developers as part of their daily workflow), and we had to scramble to restore it from backup, meanwhile no one could deploy anything.