Font files are "busy" when they are being used by other applications that are running, including the Finder. When font files are busy, the Macintosh System locks the file data internally so that it cannot be manipulated or examined in any way.
Details
FontDoctor is unable to examine any fonts that are busy, so these files are simply marked as "busy" and skipped over during the diagnosis process. This can create problems for FontDoctor later as it tries to identify fonts that are missing, duplicated, etc. FontDoctor will automatically alert you if any applications are running, and will give you the option to Quit the applications, including the Finder.
Solution
It is recommended that you Quit any running applications before using FontDoctor to examine your fonts. FontDoctor can do this for you.