Show the print object view. Window;view;other;diagnostic (Not at work, so not sure of exact name and location!) When you pick each bull clip/?mark it will tell you exactly what it is. They will be the references and relations for the object e.g. folders where the object resides, specification relation to another object.
You can ignore the warning. But, if you arent convinced create a test item, put it in a folder and then try and delete the bull clips & ?marks.