I made a simplified version that has the same problem.  I included the PDF output, the tex file, the epub, and the markdown used to generate the epub.

I zipped it all up here: https://www.dropbox.com/s/q0tjvwj2x661tb5/pandoc_sample_files.zip?dl=0

On Tuesday, July 30, 2019 at 1:52:26 AM UTC+9, John MacFarlane wrote:
Can you give us the epub -- or a simplified version which is sufficient
to reproduce the problem -- so we can see what's going on?

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