Did you find anything interesting with gdu? Can you tell me which storage your CT used to use and where you check the free space and what you see?
Since the formatting in the first post is still pretty bad maybe you can share all of these again too just so I have all the context I need
Bash:
df -hT
lsblk -o+FSTYPE
cat /etc/pve/storage.cfg
zfs list -rt all -o name,used,avail,refer,mountpoint,refquota,refreservation
local-lvm should have about 40% free space. Make sure to set up discard properly for thin-provisioned storage like that. VM-Storage seems to use pure LVM rather than LVM-Thin. I'd move the disks on it to somewhere else and re-create that if possible.
There's also what looks to be a ZFS storage but I can't tell what you use it for and how.