Tax Liability Pmt applied to Spouse SSN not TP

In a joint tax return for tax year 2018, the tax liability payments submitted with the extension (F4868) and the tax return (F1040) were applied to the spouse's ("SP") SSN and not the taxpayer's ("TP") SSN per a conversation with the Dept. of Treasury.  It was a MFJ eFile tax return. No "splitting" done other than TSJ indicators on Schedule A, where applicable. Both the TP & SP hold joint and individual bank accounts. The 2018 tax payments were made from the spouse's individual bank account.

The TP and SP discovered this year (2020), via IRS Notices, that payment was not received for tax year 2018. The married couple was penalized.

Question1: Is anyone else aware of this experience for tax year 2018 for a MFJ eFile tax return?

Question2: Does ProSeries Professional software include a toggle of sorts to indicate whether a tax payment is being paid by the TP or SP? (Not sure why this would be relevant in a joint tax return but I ask nonetheless.)

Question3: If so, how does one disengage this feature? If not, then could my experience be a fluke or a hiccup with the IRS (self-professed) antiquated platform for MFJ eFiled tax returns (for TY 2018)? This event has caused frustration to say the least. The IRS pointed me back to my tax software. No surprise. My tax software pointed me to the IRS. No surprise.

Thanks!