Comment on Notice under Section 139(9)? - Possible reason
In case you think you have made no mistake in the computation of your IT return for the relevant year then you may respond through the “Response to notice u/s 139(9)” under the E-File Section in the Income Tax e-filing portal.
In case you need to resubmit your IT return in response then you may download the returns form for the relevant year from the IT Department website and then fill it up as you would normally. Just, in this case, select the option for filing return in response to notice u/s 139(9). It is suggested you consult a CA for more insights.