Even with fairly boring usage, the Github GUI periodically wedges my repository into a state which requires CLI interaction (and a trip to stackoverflow). It's even worse for newbies - I get desperate pleas for help from clients all the time. I have come to the conclusion that there is no way around teaching the command line first, then giving them the Github client after they achieve competence.
No, I have not tried to reproduce the incidents which screwed up my repository. After a few harrowing experiences I pretty much gave up using the Github for Mac client for anything except basic commits. And even that screws up - I frequently have to commit files twice; it's like the client only stages some of the files, even though they're all checked. If my commits are large I usually go to the command line to avoid the double commit msgs. I'm about to give up entirely.
Let's be honest about git: A user unfamiliar with the CLI commands will have a difficult time, period. I hesitate to predict that it's impossible to create a good UX, but git is a very complicated system with an abstraction that leaks all the way down to database records. Breathe on it wrong and the repository will wedge into a state that sends longime veterans off to stackoverflow.
Yes, git is worth it... but so far every clever GUI has basically been a convenience tool for power users, not a better abstraction that can sidestep the learning curve. It's hard to see how this is going to change without some sort of fundamental change in git.