First of all you should have checked at the time of filing return of income whether TDS has been properly deducted or not. You should have hired a CA if you didn't knew how to do it.
However if you were filing your return yourself or your company filed your return for you and if the tax was outstanding then there would have been a pop up that this is a defective return as tax payable is outstanding.
So first check your form 26AS on income tax website whether tax is deposited and may be you have not taken the credit.
And if that's not the case then ask your department that why in form 16 have they shown that they have deducted tax and then not deposited it and ask for a refund of that TDS amount deducted but not deposited.
And income tax department will catch the employee only because at the time of filing income tax return it's the duty of individual to check whether he has got proper credit or not it's the internal matter between you and your employer and income tax department won't interfere. However if your employer has shown that TDS has been deducted and he has not deposited it then the TDS department can open a case on your employer because deducting TDS and keeping it with themselves attracts interest and penalty. How did you receive notice for A.Y. 2008-09 now?
Or were you trying to write 2018-19?
Hope you find the information helpful if you do please rate it 5 and provide your valuable feedback for my improvement.
Thank you