First TT pays nothing for you ... what you did is set up the payment instructions thru the efiling for the feds/state to complete.
If the payment was made as you directed AND you have the proof of the payment then respond to the notice with that proof ... you can try calling the number on the notice OR you can mail in a response as directed on the notice.
Depending on exactly HOW you paid via e-check, you may have mis-directed it.
IF it was an auto-debit arranged with your tax file itself...then it should be OK, and you just need to show the "IRS" proof of payment.
If you paid separately, like thru the IRS's Direct Pay website....then you might have mis-selected the payment type as a 2019 quarterly estimated payment (1040-ES) which would be directed to the 2019 taxes we haven't started or done yet, and would not be applied to your 2018 taxes.
The only other thing I could think of is that a) you put the wrong SSN on your payment, so they couldn't match it up or b) You accidentally paid your State, but not the Feds...( or paid the Feds, but not the State, and you are calling your State tax department the "IRS"...which it isn't)