CartRover is raising the following alert when trying to mark your orders as shipped:
This issue is usually caused because your WooCommerce API user is not an administrator. To fix this:
This issue can also be caused by your WooCommerce server settings blocking or removing certain header data required by the WooCommerce API.
To solve this issue, you must correct the Basic Auth header. In Apache this can be done using a rewrite rule in either your Apache config file, or in the WooCommerce .htaccess file:
This article explains the issue and several possible solutions: https://github.com/WP-API/Basic-Auth/issues/35