Good morning, @stevenkhughes02,
Let me see if I can shed some light on fees. Any time you process a payment through QuickBooks, there is going to be a processing fee. This is true of all credit card processors. I don't know of any that are free to process a payment.
This link shows the rate for processing credit cards and ACH transactions through Intuit:
QuickBooks Payments
On the same page, there is a link to processing rates for two of our competitors, Square and PayPal, showing the differences in the processing rates.
The only way to avoid any processing fees would be to accept cash or check only.
As @john-pero said, if you're just creating an invoice and being charged, then our payments support would need to look into that for you; that shouldn't be happening. Here's a link to their contact information: Contact Support
I hope that helps!