OS X 10.9.4 shows wrong used disk space
These values come from the Spotlight index. So you could try rebuilding the Spotlight index to fix these values.
There are simple instructions from Apple here on how to rebuild the Spotlight index.
You can also do it from the command line using the mdutil command. You'll be prompted for your password to run this command.
sudo mdutil -E /
Please note, whichever way you perform this task, it will take a while to run.