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Something similar happened to me in an ePub where an invisible character was used—I don't remember which one—to ensure that the em dash wouldn't separate from the word it was attached to. It looked perfect in Sigil or Calibre, but on the Libra 2 (at least in kepub format), a small, annoying blank space was displayed instead of the invisible character.
You can 'reveal' these invisible characters in the Calibre editor by moving the cursor through the text using the arrow keys, and the status bar will show you which one it is.
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