The worst has got to be ssh keys. Getting students (even Masters Computer Science students) to properly configure and handle ssh keys is the worst ongoing challenge I have.
Similarly I can use git, despite it's best efforts to be inscrutable.
But really, I find that people have trouble running ssh-keygen and then finding the key and sending me the correct one (they'll often send the private key, or more likely they'll send me both "just use the one you need".)