Taxpayers who file as married filing jointly and make the balance-due payment online may find out that their payment does not get credited to their account. This may happen if the secondary person (spouse) on the tax return makes the balance due or estimated tax payment online in his/her name and social security number (SSN) and not the primary person. The system does not reflect the payment on your taxes if you are the secondary person paying and use your name and social security number. ‘secondary’ means the second person’s name on the tax return.
The taxpayer's spouse will get a CP-14 notice saying that you still owe the balance due on your taxes. The ‘primary’ person means the first person’s name on the tax return and ‘secondary’ means the second person’s name on the tax return.
The IRS is aware of this and issued a statement on July 27,2022: "The IRS is aware that some payments made for 2021 tax returns have not been correctly applied to joint taxpayer accounts and these taxpayers are receiving erroneous balance-due notices (CP14 Notices) showing the incorrect amount. https://www.irs.gov/newsroom/irs-statement-on-balance-due-notices-cp-14
Keep track and record of all your payments and contact the IRS if you have this issue. The IRS also states that , " Taxpayers can ensure that their payment is on their account by checking Online Account under the SSN that made the payment."