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The old 0.8.6 always ran the eqivalent of Tidy beautify that sometimes ate code badly and is not suitable for epub3 at all. Sigil 0.9.3 no longer does that. Sigil 0.9.3 uses a new parser that tries to change the code being sent in as little as possible. You can beautify the entire book if you want to still via the tools menu. None of these changes should have an impact on BookView (what another ebook reader would produce).
The errors are because Finereader or whatever you used did not produce technically correct xhtml that is required by the xhtml rules. Sigil 0.9.x will autofix those for you.
The errors from epubcheck/flightcrew indicate that the epub does not meet the official epub2 or epub3 standards and should be fixed. That error indicates that you are using an anchor someplace where it is not allowed. If you click on the error, it should bring you close to the error location so you can fix it.
KevinH
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