@burlesonbrad,
TLDR; remove the shortcode, it’s not necessary and the shortcode is causing the duplicates.
The page selected as your course catalog page automatically outputs your courses without the shortcode. Why? Because using shortcodes is crude and archaic and requires you, the user, to write pseduo-html in order to do things that we can do automatically via code in the plugin.
It used to be required back in version 2.x but we changed that a while ago.
We added the ability to add content to your catalogs by adding content directly to the page you specify as your catalog page back in 3.16 (I think, I looked back through the changelog and I couldn’t find the exact point where this was added, sorry). This allows you to do all sorts of simple customizations without having to write any code.
The thing I didn’t realize is that although adding the shortcode has not been a necessity for YEARS, many users still add the shortcode anyway. Before this 3.16 update it didn’t cause any issues because the content of the page was ignored / disregarded. Users though they were making the catalog work and no one though anything of it (and I didn’t realize users were adding the shortcode unnecessarily).
Now users report duplicates, I tell them to remove the unnecessary shortcode, and life goes on. I’ve considered writing code to suppress the shortcode on this page but it seems like a lot of effort. As we burn shortcodes away with Gutenberg we’ll start to see this issue less and less (and we really don’t see it all that often).
Hope that helps,