Got the same issue, found a possible explanation: my cloud provider
store time in local timezone (earlier than UTC); at startup MySQL boot
first, then NTP, which updates the time to UTC; therefore, MySQL
literally "started in the future" (sounds interesting).

I can hotfix this by setting the timezone to UTC:

dpkg-reconfigure tzdata

After that MySQL can be stopped immediately. Even after I switch
timezone back to local time, it can still stop or restart without
problems. After rebooting the server (a KVM), I have to do this again
unless the NTP timezone issue is fixed.

BTW, @darek334:

> MySQL stops sometimes 10 minutes

10 minutes is the timeout period defined in system/multi-
user.target.wants/mysql.service (TimeoutSec=600).

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https://bugs.launchpad.net/bugs/1600164

Title:
  Mysql server take 10 minutes to stop without message after time drift

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