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:
Select all incorrectly downloaded transactions by checking the boxes before them.
Click Batch actions and select Exclude Selected.
After excluding, follow these steps to manually record them as a refund in QuickBooks.