I'm still testing Mars Edit for a 'magazine style' photoblog (on a self hosted Wordpress site) and using WP's 'post-thumbnails' feature to create and display a thumbnail image on the main page (index.php) for each post.
To automate the production of the thumbnail, I use the 'Auto Post Thumbnail' plugin http://wordpress.org/tags/auto-post-thumbnail?forum_id=10
which creates the thumbnail from the first image in the post.
This works perfectly if I use the login to the WP control panel on the site, but when I use ME, I get duplicates of both the original file and the thumbnail.
For example: (in the WP Uploads folder)
There is obviously some conflict between the plugin and MarsEdit, but I'm at a loss as to what it could be?
[Edit to fix link]