Because of my background (US Military), I am on the paranoid side when it comes to security. This has, in the past, caused issues. I once lost a drive full of files, because I encrypted it, didn’t keep a backup key, and then forgot the passphrase when I didn’t access the drive for over a month. I even wrote a script that tried to brute-force it, using variants of what I though the passphrase was.

Today, it got me again; I wanted to add some text to the footer of this site (the copyright line), and installed a plugin to do that (Footer Text). You have to edit the theme files to do that, but I was missing the Appearance -> Editor option. At first I though maybe the theme disabled it, but even going back to the default theme did not make it show back up.
After a while of searching with Google, I found an entry that mentioned a security plugin disabling the editor function. That was the clue I needed. I use the iThemes Security plugin, and had disabled the editor. Two clicks later, and I was able to edit the theme files just fine.

TL;DR I am paranoid, and it cost me at least a few hours of time today.