I think this is the least favorite of Pro/Intralink users that i've worked with, but it is a needed function to resolve missing data......A ghost object is an object without geometry. Simply put...if an assembly that you import into a workspace from a windows folder, etc is missing any parts or sub-assy's, or previously defined relationship and it is not included in the import, then Pro/Intralink will generate it as a ghost object to satisfy the missing element in the structure.
For example if Assembly1.asm has 3 parts that make up the structure named part1.prt, part2.prt and part3.prt then you import the assembly from a directory that has the assy model and only TWO of the req'd parts....say part3.prt is missing, then this will be the model that Intralink will identify and create a ghost for.
So don't just try to dismiss them entirely because they represent a missing element in your model that may need inclusion. The way to fix them is to simply import the missing model along with the rest of the assy into the same workspace before check-in to commonspace OR if you already have the missing object by name in the commonspace that is most up to date, then simply right-click on the ghost object in the workspace and choose Update Ghost Objects. If you have the needed part3.prt in this example, within the commonspace then it will correct the ghost object, if not then alternatively you will need to get the object into the commonspace via another workspace check-in with the req'd object then perform the update. Some consultant companies use special software to help aid in large amounts of this type of importing.
In case of machining model created by dependent merge option & if that cast model is renamed to some different name & now if you try to put the m/c model in workspace it will show the ghost object in the database.