3994 was a typographical error. It is 3964. I had correctly reflected it in schedule 2. Since 3964 is the total of 56 entried in 26AS from the same TAN, probably ITO mistook it. I am attaching screenshots of my ITR and the intimation I received from ITO.
I had given TDS pertaining to section 192 it in Schedule 1 and TDs pertaining to section 194A in Schedule 2 of ITR and not in one. I had attached screeshot of my ITR where it can be seen that I have filed it under schedule 2. In the case of my pension under section 192, I put it in Schedule 1.