I think I managed to fix this without breaking it LOL, I downloaded and looked at the Bestsellers Reloaded Mod, and noticed one line in how the data was pulled from the database (I am assuming LOL some things I am still taking a HUGE learning leap on!)

In includes/modules/pages/best_sellers/header_php.php at around line 32 find this line:

WHERE p.products_status = 1

and add in directly after it:

AND p.products_quantity > 0

This changed the bestseller number count to the number of products that show as having been purchased in Admin, so hopefully I fixed it the right way LOL