I had the same problem but on a custom archive-product.php page which contains a custom query to get my products with only 10 results per page.
I had 404 pages on shop page and categories page with the second page of pagination.
After analysis, I found that the main query of WooCommerce asks for 16 results but I had only 12 products in my database. So the main query returns nothing.
To change that, I need to do in admin : Appearance > Customize > WooCommerce > Product Catalog and change the value to 1 for Products per row and Rows per page.
With that the main query returns always 1 result and I had no more 404 pages.
I hope that will help you or another.
Source : https://docs.woocommerce.com/document/change-number-of-products-displayed-per-page/
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