When an order with Adjustments like shipping is refunded with the button "Quick Refund Entire Order" the return Payment amount is not correct, because the adjustment amount is not included.
For example this order:
1 product $700
S/H Adjustment: $20
Order total: $720
when refund is requested with quick refund button, the reeturn invoice total is ok ($720), but the payment is only $700. So, the invoice only have applied $700 and $20 unapplied because of payment amount.