When you go to:
SmartCrawl > Title & Meta > Posts > Post Meta Description
add the category Macro, and then look at Title & Meta Example, it outputs all of HTML
Adding trim and strip_tags to line 93 in wpmu-dev-seo/includes/core/core.php
'%%category%%' => strip_tags(get_the_category_list('','',$r['ID']) != '') ? trim(strip_tags(get_the_category_list('','',$r['ID']))) : $r['name'],
Seems to resolve the issue. But I still want to know if this could cause issues with other configurations in the future.