Notes and references seems to be omitted which are very important in some books. Ideally they should appear in the same way they appear in a Wikipedia article (as links between references and endnotes). If links are tricky, I would accept unlinked numbers (eg. [13]) and endnotes.
Topic on Extension:Collection/Wishlist
I too would love to see reference output appear the same as they do in a MediaWiki installation rather than just a URL.
I'm having additional problems too. As it stands right now with version 1.6.1 installed, the only items appearing in "References" are those URLs NOT wrapped by the <ref> and </ref> tags. An example on our wiki: http://www.limswiki.org/index.php?title=Informatics_%28academic_field%29 Only the "Further reading" and "External links" URLs are getting captured under the "References" section of the Collection output. None of the inline references (wrapped in "ref" tags) are being captured.