Site collection metrics
I am the adhoc SharePoint administrator for my department's SharePoint . I learned the share point was about full (i.e. approaching the 500 MB limit placed by the company.)
I found some areas where files could be deleted and took care of the immediate need for more space but also found some things I felt were odd.
If I go Site Actions -> Site Settings -> Storage Metrics I arrive at the Site Collection page with a list of directories and their respective sizes. The Shared Document size is currently at 553.1 MB. Yet the quota shown when I go: Tools -> About This Site shows the site has a 500 MB quota and it shows the site content to be 290.5 MB. I don't understand how this can be. Perhaps the quota is not a hard limit but will create a warning if I'm in violations for an extended period. But how can the site content show 290.5 MB when the Shared Documents directory is at 553.1 MB?
Also, when I open the Shared Documents directory I see numerous files and sub-directories along with their respective sizes. When I total the size of each of the files and directories in Shared Documents the total is over 620 MB. Again, I'm confused.
This issue you are observing may be because of backup and restore has not been done properly.Now can you take backup of your site and restore it again and let me know if you see any difference.
Please check this reference: http://sprickyrick.blogspot.com.au/2013/02/sharepoint-2010-storage-metrics.html