Update using Octopi or pacman for now.
Muon was working properly when we decided to add it to the ISO, somewhere along the line it began to break.
Upstream is looking into the current issues with Muon.
Upgraded a two-day-old install from the terminal without a hitch. System is running fairly well, but have some minor problems along with some questions. I’ll put them in another thread.
Yes, I too updated both my Manjaro KDE edition, and Netrunner Rolling 2015.09 installations using muon without any issue.
However, since some users are reporting issues with both muon updater and muon discover, I have to recommend using one of the other methods for installing applications, and performing system updates, until these issues can be resolved.
Note: If your not having any issues with muon than by all means continue using it.