Deduction U/s 89(1)

I had claimed deduction u/s 89 (1)
and duly filed and uploaded form 10E on website.

and then filed my ITR claiming such deduction.

now my ITR has been processed and when i check my Intimation of 143(1)

It shows a diffrence in refund by the amount of deduction u/s 89(1).

Why my deduction u/s 89(1) is not considered by Dept.? and
what i have to do now?