Please be very careful in these situations.
I believe we sort of stepped through this process, so I trust you are making sure that you are Enabling and Restarting your created Things before setting their Properties.
Ghost things occur when you create Things through script and the script has a mistake in it somewhere after the Create or Clone Thing happens.
Generally those indeed can be cleared out by clearing out the memory of the server i.e. restarting Thingworx or Tomcat. Please be careful though, if you restart by shutting down and starting up Tomcat, give it enough time to properly spin down and up Thingworx.
If you need help with the script you are running let us know.