Difference in backup size between Urbackup and OpenMediaVault/Linux du file usage

Hi,
Recently I noticed that my backup size reported by Urbackup and OpenMediaVault web interface or command line du or Midnight Commander are different. Urbackup statistics report about 5000 GB of file system usage, while CLI du, Midnight Commander and OpenMediaVault GUI report about 5.63 TiB of filesystem usage. That is quite a lot of difference - 5000 GB is about 4.54 TiB, so more than 1 TiB difference. I tried to use urbackupsrv remove-unknown, but it didn’t helped. I looked into backup directory and checked size of sub-directories for each user, and they are also bigger than reported in Urbackup. I’m running Urbackup in Docker, on OpenMediaVault, on Raspberry Pi 4. Disk is formatted in EXT4 format.
Edit: the difference grew over time, at beginning it was basically the same between Urbackup and OMV, I checked urbackup log directory, the log is big but not 1 TiB big

Edit: I have checked which directory is bigger than it should be, and it is the .directory_pool . As far as I know it should be cleaned from non-existing entries with urbackupsrv remove-unknown command, but for some reason it doesn’t work.

How are you measuring deduplication?

Actually I didn’t measured if there are duplicates in my data. How do you recommend to do that ? For my measurements I used ncdu command and compared resulting directory sizes with sizes shown in Urbackup web interface. I think the problem begun when I started deleting some incremental backups to save space on HDD. Normally I have incremental backup (based on last full backup) every second day, so there is quite a lot of them. After 5 months I made a new full backup, and then deleted 3/4 of incremental backups from before the second full backup. In this way I have history of changes every six day from January to June, and every second day from June until today.