Active Site Usage Not Matching Storage Used?

Hi,

You have identified the reason, document versions, but missed the bit where SharePoint will not delete extra versions already created.  What it does do is stop more than the specified number of versions existing from now on when you save a file.
You need to use powershell to go through all files deleting the unwanted versions.  We have added some extra deletion to this by deleting all versions where the last time the file was updated was more than 5 months ago.  We have many PowerPoint files in the 100-200MB range so it does not take long to consume a lot of storage with multiple versions.  We have saved TB's of space by using this script to clear versions.  We also have our own archiving process for large files, moving them to a storage account and leaving a placeholder behind.  
Do note that if using powershell you can set the version count to any value unlike the GUI which enforces a 100 minimum.  We have sites set to 20 or 50 versions and have not seen any issues with this.

Trevor