Error in tds return

In the Notice, Department just intimate us single amount of short deduction & short payment. Considering the huge data in the return, it becomes difficult to find out under what transaction short deduction is reported. On written request to ITO, they provide us party wise details of short deduction. Hence, addressing those problems becomes little easy. We need to revise the returns after making due corrections in the original e-tds return. After filing TDS returns, one should check the status of quarterly statements uploaded on NSDL website. Status of challan must be shown as “Booked”. If still it is shown as matching Pending or Amount mismatch then, we should again find out where exactly we went wrong while filing e-TDS returns. Many times due to change in software or due to ignorance, original FVU file is not available with the deductor. Then, filing revise return becomes impossible job. In such situation NSDL provides the FVU files after due registration of TAN on NSDL web site. If returns are not revised then, Assessee will be termed as “Assessee in Default” & then, order u/s 201(1) /201(1A) will be issued along with Notice of Demand by the officer. Then, only remedy available to an assessee is to file Appeal or to go for 154 Application. But if we carefully file the returns then, surely Notice from Income tax department can be avoided and then TDS job will no more be Tedious.

This doesn't answer my question.

As i had already mentined, this is a case of short deduction, & not short payment. There is a single short payment in the default file, and the challan no. is also in display. I've checked the challan status and the status says "matched"
 

We've deducted TDS after considering loss from house property and chapter VIA deductions. But the fact that these have not been considered by the IT system is clearly evident, as the amount being shown as short payment, is the tax rate on the loss from HP, chapter VIA amount.