When running a server automatic updates can be a dangerous affair. When I setup my servers I disable this feature in Ubuntu.
> sudo nano -w /etc/apt/apt.conf.d/20auto-upgrades
Change the file to the follosing
APT::Periodic::Update-Package-Lists "1"; APT::Periodic::Unattended-Upgrade "0";
Now reboot the system.
> sudo reboot
A quick change to a file. A reboot and its all done.