That is mostly since Kovid does not like adding the .DOCTYPE for unknown reasons and the cover generation/insertion routine does not add the required lines for an ePub 2 file. The first code block is what calibre uses, the second code block is what Sigil modifies it to for ePub 2 and the third block is Sigil modifies it to for ePub 3. For me, it's not worth the time and effort to argue about this, I just use Sigil to modify the code.
Code:
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
<head>
Code:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
<head>
Code:
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" xmlns:epub="http://www.idpf.org/2007/ops">
<head>
The other item is if you should be using epubcheck not the built in checker in both Sigil and calibre. If an ePub passes epubcheck, most publishers will accept it otherwise they tend to bounce for any reported error.