Total Amount Paid In 26AS Vs Income From Salary

On my 26AS form, I can see that employer has marked all the amount transferred to my account as 'Total amount paid' and didn't deduct the HRA and conveyance allowance (800 RS). However, TDS calculations are right.
Now my query is; in ITR-1 under 'Income from salary' we only mention amount after deducting HRA and CA. Will it cause any issue? or shall I only be concerned about matching TDS between 29AS and ITR-1?

Employer is suppose to deduct TDS on what he pays you. You have to provide your details to employer like lic, mf etc. to make your total taxable salary low.
But if you think that hra and transport allowances are not deducted you can always deduct and than file your return and ask for refund.

I also have the same query however the above response doesn't address it.
Problem is that form 26AS shows "total amount credited" in which my employer has put total gross salary (without deducting house rent paid). However, income tax return has "income under the head salary" which is (total gross salary - house rent paid). Hence the salary amount in form 26AS is higher than what we show in the ITR.
Is it intended by IT department that way, or is it a mistake by the employer to put gross salary amount instead of (salary - house rent paid)?

When the TDS returns are filed they are required to give total amount credited to the expense head / person and the amount of TDS. The total amount credited to you is the gross salary. So it is correct. They can not show excluding HRA as it will then not match with their financial and payroll records.