About This Mac -> Storage is wrong?
The Storage pane will show you information about files matching those categories inclusive of the entire drive, not necessarily only the files stored in those respective locations.

For example, if you downloaded a 5GB movie file, that would be +5gb in the "Videos" category, even though it might reside in ~/Downloads instead of ~/Movies

Source

That being said, your overall usage does not come anywhere close to what the storage is reporting, in terms of the entire drive having less used than you say for the Apps category alone (unless your question was not clear). To reset those values, perform a reindex of Spotlight:

Run the following command from Terminal: sudo mdutil -E /

OR follow instructions below:

Instructions