Hi Kunal,
This is the Standard accepted behavior . 1099 Vendor should be paid net of tax. Although you can change this setting
Financial Accounting Basic Settings (New)<Withholding Tax<Extended Withholding Tax<Calculation<Define Withholding Tax Type for Payment Posting
Click on FE
Change base amount from Net to Gross Amount.
and post a new invoice and clear the amount
Regards
Veenu