In this case you should file TDS return in second quarter only. TDS deduction date is for Q2, in this case software would not accept the date in Q3 and further showing the TDS in Q3 is not tenable in law.
TDS return is filed quarterly and due date for 2nd quarter(July to September) was 31/10/2019. So if you have not filed return till date, you need to file return with late fee.
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