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wyvern - I get the impression you might be importing the HTML output from Word.
If you have Word 2007 or later, you would probably be better off converting from DOCX and doing the splits during conversion, and you won't get nearly as much crud in the EPUB XHTML. There are several ways to do this:
Calibre. If you have calibre that's probably the simplest one to try.
Epub Tools add-on for Word. The Word Add-on can create an EPUB from within Word, and it has many other features, including some aimed at cleaning OCR scans, and an invaluable Dialogue Checker.
DOCX Import plugin for Sigil. The DOCXInput plugin uses the Mammoth DOCX->HTML converter, it's takes a bit of effort to configure, but if you have documents that have complex styling it might be worth the effort.
BR