/usr/bin/mysld_multi sends the processes intended to shutdown the database servers into the background. This way, when called during the shutdown sequence of the computer, a safe shutdown can not be guaranteed. In fact, if you use e.g. systemd, the background processes will be killed as soon as the script ends, which often isn't enough to even initiate the shutdown sequence of more than one server.
The shutdown part of the script MUST wait for the shutdown process to finish.
For the fix, I just removed the to-the-background part in the script, which might slow the process down a bit, because the servers are stopped in sequence. It wouldn't be so trivial to start the processes in parallel and track them all in perl, so I left it this way.
I originally found this in mysql-5.5, but I decided to post it here, because MariaDB's script has the same problem. Also, maybe somebody will be so nice as to forward this bug to the MySQL-people, because I can't register at the MySQL bugtracker because I refuse to give them all the data they require for an Oracle account, just for a bug report.