apt-get update does nothing other than updating the list of available packages, which is how the system knows when updates become available; it doesn’t actually update anything. If you meant apt-get upgrade it does actually update stuff but I personally prefer apt-get dist-upgrade as I use it all the time and have never had problems with it. The system likely crashed on you while executing the command because you had Minecraft server(s) running in the background overallocated beyond safe limits/boundaries for running Minecraft servers while ensuring proper system/subsystem operation.