Why is my MacMini always full? System Settings/General/Storage Lies!

System Settings/General/Storage says my Mac Mini has,

Mac HD (int 256Gb) 36.57Gb used of 245.11Gb

JohnD (ext 1Tb) 791.57Gb used of 1Tb

JohnDMacMiniBackup (ext 2Tb) 992.69Gb used of 2Tb

In a terminal window as root,

df -H

<<See Additional text!!! >> ARG this is so frustrating!

I'm also trying du from cron & getting this...

du: /Volumes/JohnD/johnd/Library/Containers/com.apple.mediaanalysisd/Data: Operation not permitted

 44K /Volumes/JohnD/johnd/Library/Containers/com.apple.mediaanalysisd

du: /Volumes/JohnD/johnd/Library/Application Support/MobileSync/Backup/: Operation not permitted

Needless to say /Volumes/JohnD/johnd/Library/Containers/com.apple.mediaanalysisd/Data is

full of crap I really don't want happening on this machine!!!