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Epubcheck loves to complain about hundreds of "problems" that aren't actually problems in real world usage. Unfortunately, if you want to sell through a vendor that uses epubcheck you have to jump through the epubcheck hoops, calibre will not do that automatically for you.
calibre will only produce epubcheck valid output if you give it epubcheck valid input. In this case simply replace <y> with <span class="y"> as the ducks told you. You should be able to do it fairly easily with the search and replace function in the editor.
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