The interest you pay for late deduction is a penalty levied by Govt. Hence it goes to govt. only not to the deductee. In the Challan details column it is provided but not in the deductee
Hence enter the interest in the last but one column of challan details i.e next to column no.413 (here the interest column is not numbered)
If you enter like this you will not get any difference in the challan amount and deductees total.
say challan is 1009 interest is 111 = 1120.
If you enter as said above in the deductees parcticualrs annexure on choosing this challan you get the amount of Rs. 1009 only not the 1120 paid with interest.
Hence no discrepancy will arise.
(of course you can wait for others comments)