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In some paragraphs im having hyphenation changes (as expected as it is in HTML) but the word breaking is wrong, for example, the word "outras" should be "ou-tras" and it becomes "out-ras" or "diferentes" should be "dife-rentes" but ends up "difer-entes".

The paragraph style is with the language set and it happens in more than one style.

The language is Portuguese: Orthographic Agreement
closed with the note: Find the solution, it wasn't a bug at all
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It's possible the document was configured differently from your previous ones. Here's how to set the language in InDesign:

Spell-check and language dictionaries - Set the default language dictionary for the current document