The ghost node is not an "issue" in my opinion, it's a feature.
The wcm/msm/components/ghost is a technical sling:resouceType used in MSM, when you delete component that were inherited from a Blueprint.
If the node is deleted completely on the LC, then you wouldn't see placeholders on the LC page for the deleted component, with the "Placeholder for a deleted inherited Component" message.
The idea is to leave the possibility to restore single deleted components, through this.
The wrapper might result from users/authors trying to restore the "Ghost-component" and accidentally hitting the "Target" option, instead of the "restore" option in the context menu.
If you find this could be the issue, you might want to remove the "Target"-option from the context menu, for which one option would be to overlay the ghost component "libs/wcm/msm/components/ghost" - this might not work on the apps-folder, so please try overlaying the libs-folder as a test, if "apps" does not work (even though generally overlaying in libs is not recommended - in this case this might be needed).