It wont answer your question, but you could have this problem too:
I have a problem in my current project where text frame having no text make the document report the usage of a font wich we dont want the project to use (times by exemple). The problem being that Indesign report usage of a font wich is in fact not applied to any text. Weird!
The easy fix is to identify those items (text frame class + no text) and reassign them as "unassigned".