Why is my tax return still being processed on the irs check refund website, if the money I owed was already withdrawn?

If you owed federal tax and paid it---why are you watching the IRS refund site?  What money was withdrawn?  You cannot owe federal tax AND be getting a federal refund.    Or are you referring to the fees to pay for using TurboTax?    Or are you looking for a state refund?  If you are looking for information about a state refund it will not be on the IRS site, it will be on the state site.

https://ttlc.intuit.com/questions/1899433-how-do-i-track-my-state-refund

I’m watching it because this is the first time my wife and I have filed jointly as well as owning cryptocurrencies. I was worried I made some kind of mistake. I do owe fed taxes and I was refunded state. I already received my state and that website says it’s processed. Although, if I can’t use the irs refund website for my fed taxes, how do I know they’re completed?

On the irs check my refund it says to put in, $1, if you’re refund is below 0 so I assumed it would still show the accurate status of my taxes. Is this not the case? 

You are not getting a federal refund so there is not going to be anything displayed on the IRS refund site.  If the IRS has taken your payment for the federal tax owed, you are done.   

The IRS is backlogged so transcripts are not being put on the site as quickly as during normal times but eventually you can get a transcript of your return from the IRS:

You can get a free transcript from the IRS:   

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

You can also view your IRS account online and see your payment history:

https://www.irs.gov/payments/view-your-tax-account

I actually did get the transcript already. That means it’s completed? I apologize, everything that I’ve read on checking it’s status is always associated with the irs where’s my refund website