A Gtk-Doc run generates report files inside the documentation directory. The generated files are named: <package>-undocumented.txt, <package>-undeclared.txt and <package>-unused.txt. All those are plain text files that can be viewed and postprocessed easily.
The <package>-undocumented.txt file starts with the documentation coverage summary. Below are two sections divided by blank lines. The first section lists undocumented or incomplete symbols. The second section does the same for section docs. Incomplete entries are those, which have documentation, but where e.g. a new parameter has been added.
The <package>-undeclared.txt file lists symbols given in the <package>-section.txt but not found in the sources. Check if they have been removed or if they are misspelled.
The <package>-unused.txt file lists symbol names, where the Gtk-Doc scanner has found documentation, but does not know where to put it. This means that the symbol has not yet been added to the <package>-section.txt file.
Enable or add the TESTS=($GTKDOC_CHECK) line in Makefile.am. If at least gtk-doc 1.9 is installed, this will run sanity checks during make check run.