Thanks for reaching out to the Community, TaylorHeating. I appreciate your detailed information.

Credits won't be applied to invoices while editing them, however it's possible you've opened the Receive payment screen for your invoice. Doing so, while your Automatically apply credits setting is turned off and a credit exists for the customer, will show a Credits section and QuickBooks will automatically select a credit to apply to their invoice.

You can click the credit's checkbox to unselect it. This way no credit will be applied to their invoice.

I've also included a detailed resource about working with invoices which may come in handy moving forward: Create & manage invoices

Please don't hesitate to send a reply if there's any additional questions. Have a lovely Monday!