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If you are doing your formatting using the toolbar instead of paragraph styles in Word (or any other word processor package), your behind-the-scenes code is likely to be a supreme mess when converted to html in the epub. There is no way to fix this with a conversion. You either have to use styles exclusively in the source document, or edit the epub later to fix it.
And some word processor items (tabs, most auto-numbered lists, etc.) either are ignored or not allowed in html, so they can cause very strange things in conversion.
There are also settings in the Calibre conversion that might cause what you describe; for example try turning off all structure detection and see how it looks.
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