Did you actually make an estimated tax payment (Form 1040ES) on 4/15/2019 or did your instead make a payment with a request for extension (Form 4868)? These two types of payments are different and reported differently on your tax return. On an 2018 tax return, estimated tax payments are reported on Schedule 5 line 66 and payments with extension are reported on Schedule 5 line 71. These are each entered differently into TurboTax to cause TurboTax to put the payment on the correct line. If it's on the wrong line, its possible that an IRS system and examiner might not recognize the credit for that a payment. Also, if you made an estimated tax payment rather than a payment with a request for extension, it's possible that the IRS credited it to 2019 instead of to 2018.
I suggest obtaining the transcripts of your tax account for 2018 and 2019 to if and how the payment was credited: https://www.irs.gov/individuals/get-transcript
