Not sure why @mattwiebe found this to be an improper bug report, because I'd spent quite some time asking around about the cons of using post_content_filtered over post meta or something like that. IMO, that was a single bug, anyway, since you asked specifically, here's one instance where the Markdown content is lost and HTML content is shown instead in the post editor.
Editing a post using 'Quick Edit' option on the 'All Posts' screen, for e.g. to change title, slug, adding/removing categories and tags, etc., seems to remove the Markdown content. So when I open the post (edit screen) I see HTML instead of Markdown.
This happens on WordPress.com too.
Confirmed on JP 2.8/WP 3.8.1 and WP.com, specifically when adding/removing category or editing the page title. Simply adding a tag didn't do it.
Unload Markdown when bulk editing
Markdown: unload Markdown actions when bulk editing to avoid losing M…