Hi @flyfisher842,
MP 3.0 was rewritten from scratch but it still uses WP practices for changing archive pages and that something Clean Retina doesn’t handle well.
I did a test on my installation with “Enhanced Category Pages” plugin that allows you to edit category pages and this plugin works fine on default WP themes but it also doesn’t work with Clean Retina theme which points to the theme being the issue here.
You can create custom template for MP categories page by creating mp_category.php file in your child theme root folder but you will need to check with the theme devs about what code needs to be added in there in order to override theme default behaviour.
Cheers,
Predrag