If I add a subtitle with Sigil by adding the metadata for Title, then add to that the property for subtitle, that subtitle needs to be after the main title in the content.opf; it it's before the main title then Calibre displays the subtitle as the book's title. Maybe it's in the epub 3 standard that order is significant for title and subtitle?
Subtitle first:
Code:
<dc:title id="tle">Subtitle</dc:title>
<meta refines="#tle" property="title-type">subtitle</meta>
<dc:title>Main title</dc:title>
Main title first:
Code:
<dc:title>Main title</dc:title>
<dc:title id="tle">Subtitle</dc:title>
<meta refines="#tle" property="title-type">subtitle</meta>