I\'m using:
I register custom taxonomy (catalog)
What helped me is to set "Blog pages show at most" in Reading Settings to 1. Then it works.
With the default 10, it throws 404 error on page 2. On page 1 it's all perfect.
So given this works, the solution is to set "Blog pages show at most" to 1 only for those taxonomies or categories you need. The code you should place inside functions.php is here: https://forums.envato.com/t/wordpress-custom-page-type-taxonomy-pagination/76549/12