When you connect your store using shopping cart plugins (e.g. Magento, Shopify, eBay), AfterShip will automatically detect the courier of each shipment based on its tracking number format. While AfterShip supports over 300 couriers, the same tracking number format may match multiple couriers.
In this case, you should specify the couriers at settings, and also put the more important courier at a higher priority. If this still could not solve your problem, you should consider adding the tracking number with the courier slug.
Refer here to know more about how to add tracking numbers in AfterShip.