How do I clear this up? I had to pay additional taxes for 2021 but the IRS never applied to my account even thought they deposited it and now say I owe more.

first I would contact audit defense because they handle it. 

you can also use the IRS website to view a transcript of your 2021 account.

it's important to find out where your cheek was applied so. it might be necessary to call the IRS if it doesn't show up in your 2021 account. For this you'll need a copy of the bank statement where it cleared. it will have identifying characters which an agent will need to track it down. the agent may be able to correct any misapplication

https://www.irs.gov/individuals/get-transcript  

Call 800-829-1040

• Choose your language,
• Then choose option 2
• Then 1
• Then 3
• Then 2
• When it asks you to enter your SSN or EIN do nothing – wait - - After it asks twice, you will get another menu
• Then 2
• Then 3

It should then transfer you to an agent. Note when its phone line are busy you may be on hold for a long while or disconnected