Two form 16 but itr filled for only one form 16

You have to file ITR for Both the FOrm 16

You have to check the contents of the 143 intimation and column by column see where is the difference. The logic that you have given for not filling both the form16 is very strange. In Income tax arena, few logic works, you have to go by whats black and white, anyways if you had cofusion that time was right to come to this forum and ask. 

you have to file a rectification in response to section 143(1) notice. & mention the correct income in that rectified ITR. consider the income shown in both forms 16. & also the TDs deducted by both the employers.

File a revise return and fill both form 16 details in it. It is incorrect to show incomplete details. Kindly revise the return at the earliest. Pay the necessary taxes as applicable.

I agree with Kaardaata. If you had some confusion at that time, you should have come to the foum and ask then. 

Kindly revise the return at the earliest