When System Updates (PUM) installs available updates in Plesk when it is configured to automatical mode?
When System Updates (PUM) is setup to automatic updates, it checks for new updates once a day during the daily maintenance task and installs any updates that are available immediately. So any new updates that should be installed will be in fact installed right away after they are detected during the daily task process.
So if there are some tasks being performed at the moment when system updates are installed, tasks may be interrupted or stopped. This is an expected behavior as this is how package managers (like yum or apt-get) work. So PUM is basically the same functionality that "#yum update" provides.
To prevent any possible issues caused by installing system updates, turn off the automatic mode in order to update system packages manually:
Alternatively, you may lock a certain package (or packages) to prevent it from automatically updating.