I am certainly not an expert on hyphens - I don't use them, I prefer ragged-right. But boxes, or other symbols like that, usually happen when the symbol it is trying to use is not supported by the font.
I would start by removing any custom font, and just use a standard/default one. If that doesn't fix it, I would test by changing the language settings you are using. Perhaps the language is trying to use a non-standard hyphen symbol??
edit:
Welcome to MR!!
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