Sites using post excerpts on homepage panes are having all the post excerpts, plus any plugins that appear after them, repeated. This has been noted in several blogs using excerpts here:
I have also noticed it duplicating action hook widgets on a post.
The only thing I have seen changed in the changelog is a change to the copyright text and fixing an XSS vulnerability. It is probably related to the latter.
This has also been reported in the WordPress Graphene forum; I have let users there know to follow this thread.