I have just experienced my first run-in with these ghost parts. I poked around on a lot of websites and found a few fixes. The only thing that worked for me though, was to add two options to the config.pro file. The options are cleanup_drawing_dependencies and cleanup_layout_dependencies both should be set to yes. I had to open both the layout and the drawing, regenerate, and save both files. I could then delete the ghost objects from my workspace and they haven't come back yet. Shoot, I better find some wood to knock on! Good luck.
I had the same problem when I updated proe to the latest release before wildfire, Tech support told me to set cleanup_drawing_dependencies and open_simplified_rep_by_default to yes, fix these ghost objects, as Jharroun stated, but to return cleanup_drawing_dependencies set to no after the ghost objects are removed.
I found that these ghost objects always existed but were forced in if you were logged on as admin in Intralink.