A guess, based on the fact that the question marks seem to come between syllables: perhaps your books use the HTML soft-hyphen entity to indicate possible end-of-line word breaks; and perhaps Digital Editions can't interpret it, and renders it as a question mark. You could check by opening the extracted HTML in a text editor (or open it in a browser and use the view-source setting). The fix, if this is the case, would presumably be a global search-and-delete of the entity in the HTML files, since you probably can't change DE's behavior.
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