Let me help you fix this, @Jacob Dornbos.
The way QuickBooks recognizes downloaded bank transactions depends on how a financial institution import them in the system. I recommend reaching out to your bank to check why these transactions are being downloaded as payments instead of refunds.
Although, we can still fix this by excluding these transactions and record them manually in your bank register.
Here's how to exclude transactions:
After excluding, follow these steps to manually record them as a refund in QuickBooks.
You can also assign and categorize these transactions to easily review the information you've received from your bank.
I'll be around if you need anything else.