We run epubcheck on uploaded EPUBs as a courtesy, since setting up epubcheck to run yourself can be a pain.
If your EPUB file loads in iBooks then you can get away with ignoring the errors in some cases, but just note that some of your readers may have issues. Also, note that other stores such as the iBookstore reject EPUB files which fail epubcheck, so it's a good idea to ensure that you pass epubcheck.
Unfortunately, we can't provide support for debugging uploaded EPUBs and epubcheck.
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