Open Disk Utility and run the repair option. Start there.
If nothing, open the Finder and make sure you are in the root view (Macintosh HD); select List view; click on the Action menu; click on Show View Options; make sure that Calculate All Sizes is checked; Sit back and wait. Could take a while, but this will sort and organize all files by size. If there is a permissions issue or some other weirdness, then it will take a while. This option forces the system to accurately calculate the space each file is taking, and could take hours.
You may learn nothing, you may learn everything.
