rss-functions.php parses Atom feeds by abstracting them to RSS feeds. Atom feeds can have multiple link elements, and rss-functions.php tries to handle this by selecting only the links that have the attribute 'rel'=='alternate'. The problem is created when the atom feed has multiple link elements with that attribute set. For example, a feed might have /feed/entry/link/$attr[rel]='alternate' AND /feed/entry/source/link/$attr[rel]='alternate'. Currently, rss-functions.php inadvertantly concatenates the two together.
I discovered this when using a shared feed from Google Reader in an RSS widget.
Example feed: http://www.google.com/reader/public/atom/user/07602940155368702956/label/www