I paid my taxes when I submitted my e-file return. l just received a notice from IRS saying I still owe. Has anyone else had this issue?

[Critter-3]

Many have ... seems to be a current  IRS issue for some folks  ... so get your proof of payment in hand and call the number on the notice to get this corrected.   Or mail in a response as directed on the notice.  

[rjs]

Yes, there have been a number of similar complaints. How did you pay the tax that was due? If you paid by direct debit, was the payment taken out of your bank account? If so, you should be able to reply to the IRS notice with a copy of the bank transaction record, showing that the payment was made. Read the entire notice carefully, and follow the instructions in the notice for how to respond. Send your response by certified mail with a return receipt, and be sure to respond by the deadline in the notice.