Ya thanks for that. I actually figured out the issue. Using ncdu only shows the storage used in the home directory. Using " ncdu -x / " shows the storage used by the whole directory.
and I Identified the proplem was using a software called "timeshift" which its purpose is to backup data. And its automatic backup option was on and all my data has been backuping in background on a 2-3 day base over and over.
I deleted the unnecessary backups and changed the backup routine option to once in a month.