PHP Markdown's issue with the way WordPress processes text

Aahan, this is an issue with the assumptions that WordPress makes about the state of its content, and how MoSI works.

WordPress assumes that there will be no p tags (since that’s the way WP normally does things) and that’s the assumption that Twenty Thirteen is making when it appends the date to an aside post format. It thinks that the date will simply be caught up in the last paragraph, but instead, since MoSI creates p tags, it winds up outside of the last paragraph.

This could be worked around if need be, but it’s not really a plugin bug.

Asking the Markdown Extra author to fix this is the wrong approach. It’s not a problem with Markdown Extra, it’s the clash of assumptions I already outlined above. Basically you need to strip the p tags created by Markdown, and then re-add the wpautop filter that MoSI removes.