Wrong Withholding Tax Calculation Upon Application of Prepayment Invoice To Standard Invoice

In our Environment, we have enabled Automatic Withholding Tax is Enabled at 'Invoice Validation' Stage and here is the flow,

Step 1: Creation of Prepayment Invoice to Vendor : INR 10000

Step 2: System Applied the WHT (10%) and Created a WHT Invoice for INR 1000

Step 3: Processed the Payment for Prepayment Invoice (Adjusted Balance) INR 9000

Step 4: Created a Standard Invoice for INR 15000

Step 5: Before Validating the Invoice, Applied the Prepayment Invoice fully

Step 6: System Applied INR 10000 to the Standard Invoice of INR 15000 and Created the WHT Distributions as below

a) Two WHT Distributions are created, one with INR 1000 & Other with - INR 500

b) Total Standard Invoice Balance Adjusted to INR 5500 (Looks Weird)