If you are using lab-fulfillment via the Pixieset Store, the "Pixieset Application Fee" you see in the Stripe dashboard is your Cost of Goods Sold that we forward to the printer (WHCC or ProDPI in this case). Instead of billing you for the print cost at a later date, this is taken when the order is placed, and what you received in your account is all profit (minus taxes).
If you add up the cost of prints and shipping, it should equal to exactly the amount of "Pixieset Application Fee". You can view a detailed breakdown of this amount in your Pixieset dashboard. Go to the specific order and click on Cost of Goods Sold amount at the bottom of the order receipt.