You might need to forget the package. :EDIT
Every package installed via Apple tools is recorded.
You can use pkgutil
to find out which files were installed.
man pkgutil
pkgutil --pkgs #the packages installed on the system
pkgutil --files package-id # installed files
Remove these files. Job's not quite done, though. Depending on your use case, you might want all knowledge of this install to be removed.
pkgutil --forget package-id # this never happened.