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That's happening most likely because you're not also using the original site's css. Without the original css an html page will often look nothing like the original formatting on the web.
Anyway just saving the html is not generally the best way to convert a site to an ebook - you should read up on creating recipes, and then create a recipe for that site, only extracting the data that's pertinent to the ebook from the site and leaving the rest of the interactive cruft out.
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