Rebate U/s 87A effect on TDS

Yes, You can calculate accordingly.

 you can apply for refund ,   if  TDS  deducted  and  your  Income below 500000/- 

Thanks , actually in this case tds was not deducted by employer giving effect to 87A as total income of employee below 5 Lakhs , so I was concerned about any default on part of employer for non deducting tds .

I think  he  has to deduct  TDS  however , Can't do any thing now   , If  not  deducted   .  If  your income is bellow 500000/- whole  Tax amount will be wipe out  against  rebate under section 87A  of the Income Tax act . However ,  since   your income is more 250000/- you have file return for F.Y 19-20 . 

Does employer have to face any consequences for non deduction tds if employee filed his return within due date.

If income is below 5,00,000 than Employer is not liable to deduct TDS, as there is no tax TDS (have to consider rebate u/s 87A for calculating TDS Liability).

Second, if income of Employee is more than 2,50,000 than Employee is required to file income tax return, inspite of there is no tax payable/refundable.

Thanks , also Employer didn't file tds 24q return in this case showing salary , deductions , and rs.0 as tds as no tds applicable for all his employees
is it ok ?

No. Employers can not consider rebate u/s 87A and have to make TDS from the salaries of the employees without giving effect of such rebate benefit. Some Accounting Software Firms have been noticed by IT Dept. for doing so.