Comment 10 for bug 52685

I had a similar problem when a file belonged to a package (according to dpkg -S) but it wasn't a part of current version. Try to manually remove (sudo rm) all duplicate files (from both x11-common and xinit packages) and then reinstall both packages (sudo apt-get install --reinstall x11-common xinit). This should probably remove duplicate files for you and install the right ones.