Open Question: One deduct TDS on the whole amount of bill even one issue debit note against the same bill, is this correct?

Dear All, Here is a organisation which deduct the TDS on the whole amount of bill he credited and also issued the debit note against the same bill. Is this correct practice? Suppose: Bill amount is Rs. 50,000 .00 Deduct TDS Rs. 1000.00 ( 2% of whole amount) Debit Note Rs. 5000.00 Made Payment Rs. 44,000 .00 Kindly refer me income tax section, If it is wrong. Looking forward to your valued reply. Regards