A WooCommerce orphaned variation is a variation without a link to a parent product. This can happen sometimes during updates, or data manipulation and it’s recommended to not keep them in the database to avoid any potential errors on your e-commerce site.
Here are two SQL queries that you can run on your database, the 1st one will allow to select those orphaned variations, and the 2nd one can be used to delete them. In all cases, please do a database backup before taking any actions:
Select WooCommerce Orphaned Variations
Delete WooCommerce Orphaned Variations