You should check if M2E Pro Shipping is enabled in the list of shipping methods for the Magento Store View where an order is being imported.
To do that, navigate to System > Configuration > Sales > Shipping Methods > M2E Pro Shipping tab (for Magento 1), or Stores > Configuration > Sales > Shipping Methods > M2E Pro Shipping tab (for Magento 2).
For Amazon integration, you should also configure Shipping Mapping settings by linking Amazon and Magento shipping services. This way, you can ensure that the correct shipping service is used for each order.
Navigate to Amazon Integration > Configuration > Shipping Mapping. There, you’ll see all available delivery types for Domestic and International services depending on the Amazon marketplace. For each delivery type, you should select the corresponding Magento service from a dropdown menu.
The shipping service data will be imported to Magento orders according to your Shipping Mapping settings.
Another reason for this error is an external shipping extension installed in your Magento which overrides core functionality.
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