Intimation u/s 143(1)(a)

This is a query for the AY 17-18.

I have filed my returns by referring to form 16 given by the IT department.

The total income was 10 lakhs and the exception under 80c was 1.5 lakhs plus the exemption under section 10 was 2 lakhs. So the total taxable income would be 6.5 lakhs. 

The form 26AS shows the total income paid/credited as 10 lakhs.

Here is my query.

I received an intimation from the IT department citing "There is inconsistency between salary income in return and Form 26AS" u/s 143(1)(a) of Income Tax Act, 1961.

I logged-in into my IT account and looked at the intimation under e-proceeding. I could see that the total taxable income was showing as 8.5 lakhs instead of 6 lakhs. They did not consider the exemptions under section 10. I disagreed to this notice and entered all the details under section 10.

After a few months, I received the same notice, again I disagreed to this intimation too.

They were not satisfied yet. Recently I received a letter citing there is still inconsistency. As per my knowledge, I need to file a rectification for this. Please correct me if I am wrong or what action I need to take to close this proceeding.