That’s not an error message but rather a boot-time informational message that your filesystems checked out clean. This is normal, because Manjaro automatically checks the filesystems for errors at boot time.
The fact that you are seeing this message at shutdown is simply because the console buffer with the boot messages is not wiped, but instead remains in video memory somewhere in the background ─ it’s a tty, i.e. a character-mode virtual console, which is a very different thing to the graphical session of your desktop environment ─ and so when the system shuts down, it kills the graphical display server and switches back to the boot-up console.
The message therefore is not generated at shutdown, but at boot time. 
Breaking this down into two parts…:
1.
The Stable branch of Manjaro doesn’t get updates as often as Arch, because Manjaro is a curated rolling-release distribution. This means that new packages are tested much more extensively in the Unstable, Testing and Stable Staging branches ─ the latter is an unofficial experimental branch for those seeking to experience the bleeding edge in an otherwise Stable installation ─ before they are pushed out into Stable proper, and when they do, they are bundled together.
Three days ago, there was indeed a major update to Stable, as you can read in this thread here.
Bundled updates are always announced by way of such dedicated threads. I recommend that you subscribe to notifications for the Stable Updates category. That way, you’ll be able to glean some important information about each major update.
2.
I’m not sure what caused that error for you concretely, but the cause could be a network problem, or perhaps a problem with the primary mirror in your list. You can usually resolve that by issuing the following command in a terminal ─ note that it takes a bit of time to complete, so do not interrupt the process…: 
sudo pacman-mirrors -f 5 && sudo pacman -Syyu
If these drives are mounted via /etc/fstab ─ and that is really the best way to do it ─ then you can add nofail to the mount options for each of them. That way they won’t stall the boot process if they are offline.