Shopify's fees are taken once every 30 days.

When your billing cycle is over you will be sent an email which will contain a link to a page in your admin site that shows all the transaction fees that have been billed for your sales. 

Shopify charges its transaction fees on the total size of the transactions (cost of products - discounts + tax + shipping).

To dispute transaction fees for reasons such as returns or non-payment, you will need to cancel the order.