If you notice an unexpected amount of your server's disk being used, you can run the command line tool ncdu to track down what is consuming the most disk space.
First, SSH in to your server as root and run the following command to install ncdu:
sudo apt-get install ncdu
After ncdu is installed on your server, run the tool with this command:
sudo ncdu /
ncdu will scan all the files on your server's disk.
When it finishes, it will display your results with the directories and files listed from most disk usage to least disk usage. You can then easily navigate through ncdu using your keyboard's arrow keys and look for any files that are using more disk space than you expect.