If you add some File over SSH or FTP to your Owncloud Data-Folder you will not see this.

Login via SSH and got to the OwnCloud Root Folder and Enter these Commands

php console.php files:scan <user_id> #For rescanning a users file
php console.php files:scan --all #For rescanning the files of all users

or if you using MySQl Database, run these SQL-Command:
TRUNCATE oc_filecache;