Looking at the XML output of Epubcheck 4.0.2, sometimes the value of the "severity" attribute in a message element contradicts the actual warning/error message. To illustrate this see below EPUB:

epub20_crazy_columns.epub

I run this through Epubcheck using:

java -jar epubcheck.jar epub20_crazy_columns.epub -out epub20_crazy_columns.xml

The output contains a validation message about about the use of absolute positions:

<message severity="error" subMessage="CSS-017">CSS-017, WARN, [CSS selector specifies absolute position.], OEBPS/Styles/styles.css (13-1)</message>

It is strange that the severity attribute states that this is an error, whereas the text message says it is a warning. Seeing that this file passed validation I'm assuming that internally Epubcheck considers this to be a warning.

Another example is this file:

epub20_encryption_binary_content.epub

Here Epubcheck reports:

<message severity="error" subMessage="HTM-023">HTM-023, WARN, [An invalid XHTML Named Entity was found: '&amp;0;'.], OEBPS/Text/pdfMigration.html (18-197)</message>

Which again shows the same problem.