I just discovered a similar flaw.  I believe that older versions of QuickBooks allowed you to run a transaction detail report by vendor, and it included payments & refunds.  It's changed.  QB Pro 2017 only allows you to run reports for payments TO the vendor.  I don't use bills, invoices, etc.; only the checkbook.  If I include a refund from a vendor on a deposit slip, the amount WILL NOT appear on that transaction report.  The only way to "hunt" for the credits is to look at the expense category and sort by Vendor.  It will appear there.  I believe this to be a flaw in QB.