Any used space that is not accounted for by GrandPerspective based on the size of all files it scanned is dubbed miscellaneous used space. Basically, it is unclear what is taking up this space. So if there is a lot of miscellaneous used space and you want to find out what it consists of, you need to scan more. More specifically:

• Scan your entire volume, not just one of its folders
• Use the physical file size measure
• Do not use a filter, i.e. do not use Filtered Scan
• Ensure the application has Full Disk Access

Grant GrandPerspective Full Disk Access

You should grant the application Full Disk Access. This can be done via "System Preferences" > "Security & Privacy" > "Privacy". In the permission pane at the left, find "Full Disk Access" and select it. (Note, this permission setting is only available in recent versions of macOS.) Click the lock to make changes, and add GrandPerspective to the application pane at the right; you can do so via drag and drop.

Limitations

Even with Full Disk Access enabled, GrandPerspective cannot read all files. In particular, it is not able to scan the following:

• Files owned by other users. These can be scanned by letting their owners scan their home directory themselves
• Certain system files. Data Vaults, for example, are directories that are only readable by a process that has a specific entitlement. Being root will not give you access, nor will enabling FDA.