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First of all iBooks has it quirks and strange way of working. That being said, I don't think it is your problem in this case.
If you use Word, it is good to save it as filtered HTML. However, even that file is really bloated and contains tons of unnecessary code which can cause unexpected effects in rendering on readers. Using Calibre to convert will not help you there.
If you really want to solve this, there is no solution but to clean either the ePUB or the HTML export of Word.
If you don't want to look at the code at all, download and use Atlantis Word Processor. Load your Word document in that. Check your layout and then you can save as ePUB.
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