Incorrect free disk space on SSD after cloning Yosemite partition because of corrupt ".Trashes" folder
Ha, found it! It was a corrupted ".Trashes" folder in the root of the SSD. It occupied me than 100GB of data (see screenshot).



I managed to make these files visible by running GrandPerspective from the command line:

sudo GrandPerspective.app/Contents/MacOS/GrandPerspective


That will show the files but still it is not possible to delete them.
Even

sudo rm -rf /.Trashes/*


did not work. It just returned immediately without any output.
The solution was to have Terminal run as root and then delete, so start Terminal and run:

sudo /Applications/Utilities/Terminal.app/Contents/MacOS/Terminal


Then, in the "root" Terminal window:

rm -rf /.Trashes/*


Running GrandPerspective again afterwards shows only 16MB of miscellaneous space.