Tds lower deduction certificate issued by ito backdated

Ajayraj (F&A) (55 Points)

25 September 2015  
ITO issued to a party short deduction certificate on 11th of September instating that TDS is to be deducted at a lower percentage from what required, now the party want us to give credit note of that amount.
So what can we do? and what to do with TDS returns ?
can someone help