By default, Disk Graph can only show files that are not protected by the operating system, which will result in the graph showing more free space than expected when scanning directories such as /Library or /System. Starting from macOS 10.14, you can grant access to these protected system files.
- Go to System Settings > Security > Privacy.
- Click on the lock at the bottom left of the window and enter your system password.
- Click on the plus button and select the application.
- Click on the lock again. You can now close the window.