Warnings mean there are links to destinations that don't exist, not extra destinations.
A named destination beginning with G is automatically created for every paragraph that contains a cross-reference or hypertext marker or is the target of one of the hypertext markers Frame put in the TOC or index. For example, G11.1004347 would correspond to a paragraph having object ID 1004347 in the 11th component of your book file.
A missing destination warning will result if you either delete or move the target of a TOC or index link after generating those files. They can also indicate that old, no longer valid links have been left behind from previous generations of the TOC and index.
Regenerating your TOC and index might fix most if not all of your hypertext invalid links. If not, you can search your book for the problem markers by using the find marker text option and entering each of the paragraph IDs listed by Distiller. For example, to find the marker that specifies G11.1004347 as a destination, search for marker text 1004347.