Query re. response to cpc communication -incorrect claim u/s 143(1)(a)(ii)

1. In my ITR-2 for AY 17-18, I had erroneously shown the CG u/s 54EC, instead of what should have been u/s 54.
2. I received a communication from CPC, pointing out “Incorrect Claim u/s 143(1)(a)(ii)”, as under:

• In order to correct the error, I have filed a Revised return, with the correct Section indicated;
• However, in the online response to the communication there were only 3 options shown:      

                                 -- Agree (Please file a Revised Return)

                                -- Partially Agree (Please file a Revised Return)

                                   --Disagree

• Since, I was filing a Revised return, and the CPC Communication was correct in terms of there being an error, I have marked “Agreed” and submitted the response.
• But I now have a doubt – should I have chosen the option “Disagree”? If so, what can I do now to correct the status. The Revised Return already filed has corrected all errors.

Grateful for any guidance.