It is common knowledge for Arch based distributions - the command to update your system is
pacman -Syu
That is the correct command - one should never sync new packages unless the whole system is up-to-date
That is expected as you issue a command to sync updates and add packages
Why does it make you nervous?
Thats not a problem because all packages are downloaded before the actual update transaction begins.
That is because you interupted the transaction - so your action caused your issue.
There is - if you use btrfs and and timeshift
The suggestion did not crash your system
It is a completely valid sync command - it is your subsequent actions which caused your system issues.
Let clear something up for you.
Manjaro Linux is not blame for your problem - you can only blame yourself.