Comment 16 for bug 1554795

I had the same issue, too...
Lots of messages saying "Timed out stoppping ...".
The system never rebooted.

Here is what fixed the problem for me:

Firstly, I activated systemd's debug shell using 'systemctl enable debug-shell.service'.
Then I initiated a reboot and when the problem occured, I switched to debug shell (alt+F9 [/F10 ?] ).
Using 'systemctl list-jobs', I figured out what jobs were running while the system hung.

One of the jobs was an "unattended-upgrdes" job.
This job held one ore more files on my root filesystem open.
When I killed that process, the system finished its shutdown and rebooted.

After having removed the package by 'apt-get --purge remove unattended-upgrades' the problem didn't arise again.

I am using cron-apt on my servers - therefore I do not necessarily need unattended-upgrades.

Hopefully this helps as workaround and to find the real cause of the problem.