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Don't use Calibre to make your ePubs if you're trying to make beautiful books. I love the program, but it uses a lot of workarounds in an effort to cover the massive amount of garbage that it gets fed. It's perfect for a quick conversion and transfer for reading.
Edit in a text editor (NoteTab!) as spare, strict XHTML, with good CSS and excellent structure. Import to Sigil, add your breaks, semantic content, edit your TOC, etc., etc. and save as ePub.
Don't use something that Calibre created for you as a source in Sigil -- it's going to be unreadable in code view, and force you to edit visually instead of logically.
The next version of Sigil is going to have an ePub checking library, I think.
That said, if you use Linux, the Dillo web browser has an excellent XHTML checker built into it. Launch a page and the bugs show up in the lower right corner -- click on that and it give you line numbers with errors.
$0.02
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