It is very much clear that Income Tax Department charge Interest on all late deposit TDS/TCS.  In case we have deposited interest amount on a challan no 281/e-payment.  Now a  following question arise that 

Question :-  Should we enter interest challan entry while submitting  etds/etcs return ?
Answer   :-  "Yes".  It means that entry is must in e-tds/e-tcs return even there is TDS amount is nil only Interest amount is available.  Picture view of entry is also given below :-

In this way only challan entry will be made in Challan Detail and there will no entry in Annexure-1 or Annexure -2 in NSDL software.
Secondly, form 16 & 16A programme is also updated accordingly.   Earlier there is problem due to this type of entry but now the same has been resolved.