Payment fees
Ask your finance team what the terms are for your payment processing. Stripe, for example, charges around 1.5% + 20p per transaction for standard UK cards, and more for international cards.
Example
Shipping fees
You might set a default shipping rate for each sale, but you may have to subsidise this. Are you accounting for it?
Simply add up all of the courier charges you paid for every order, then check what shipping revenue you collected. If the courier fees were higher, the difference is the subsidy. To calculate it per order, take the extra charge you paid and divide it by the number of orders. That’s your subsidy fee.
You can add this to your costs and spread it out over every order. In time, you could get more granular and work out the subsidy per product.
Example