Comment on Notice under Section 139(9)? - Possible reason

Hi All,
I have received notice under 139(9) for rectification.
I am a salaried employee, for last year assessment I had two form 16 from my previous company and from my current company.
When I filed ITR and got some positive amount in payable with that Payable amount balance I have submitted my ITR.
Now I have two question
1. When I am salaried employee and my tax already has been deducted from source side, then how it could be possible payable comes as positive amount. I can guess because of salary increment there are some amount need to pay.
2. If I want to pay payable online then how to pay… what chalan should I select, what TAN previous company or current company after payment then how to upload the xml finalise everything

I will be highly obliged and thankful for kind helpme

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