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I spent some time studying the gumbo code to see under what condition it tries to create a comment.
It seems that an xml "processing instruction" is now illegal in html and html5 and so gumbo will convert those to comments <!-- blah --> so that they are not lost.
So someplace in the original xml was a <?p> xml processing instructions meant for an external xsl stylesheet that got converted to <!--?p-->.
Something in ePubTidy or some other plugin that "smartens" things must have converted the -- to emdashes or endashes given what DiapDealers says above as gumbo just produces normal dashes when creating a comment.
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