1) If you run epubcheck on the EPUB file you attached, you get:
Code:
$ epubcheck 9781621374008_EPUB.epub
Epubcheck Version 3.0.1
Validating against EPUB version 2.0
ERROR: 9781621374008_EPUB.epub/OEBPS/content.opf(84,79): 'a4': fragment identifier is not defined in 'OEBPS/Text/toc.html'
Check finished with warnings or errors
You need to check your content.opf file, which is referring anchor 'a4', which indeed is not present in toc.html.
2) The spreadsheet you linked contains indeed only 1 line referring to EPUB file 9781621374008_EPUB.epub --- all the other lines seem related to other EPUB files.
3) Complain with Apple for their poor error reporting.