I'm being charged twice for what I owe Federal taxes. I paid the $47 owed using my credit card and it was also taken out of my state refund.

Your state tax due cannot be paid from your federal refund.   Your federal tax due cannot be paid from a state refund.

It is not possible to pay your state tax due from your federal refund, nor is it possible to pay a federal tax due from a state refund.  The federal and state treasuries are completely separate from each other.  You may have seen a TurboTax summary of your federal and state amounts that confused you into thinking one was “paying” the other.  It is not. The ONLY thing you can pay for from a federal refund is your TurboTax fees if you chose that option.  

 If you have federal tax due you can pay by mailing your payment with the 1040V voucher, (which has the address printed on it, having the payment taken out of a designated bank account, or you can pay directly on the IRS website. 

https://www.irs.gov/payments

https://ttlc.intuit.com/community/tax-payments/help/how-can-i-pay-my-federal-taxes/00/26212

https://ttlc.intuit.com/community/tax-payments/help/how-do-i-pay-my-irs-tax-due-with-a-check-or-money-order/00/26403 

To apply for a payment plan with the IRS

Apply Online for a Payment Plan

You must pay your state tax due using the state’s preferred method of receiving payment.  For most states that will be by making a payment to the state’s own tax website, or by mailing a check or money order.

https://ttlc.intuit.com/questions/1900884-what-are-my-options-for-getting-my-state-refund-or-for-paying-any-state-taxes-i-owe

https://ttlc.intuit.com/questions/1901670-how-do-i-contact-my-state-department-of-revenue

If you are looking at the Refund shown on the Tax Home web page, that is the Net between the tax refund and the taxes owed.  It in No Way means the taxes owed were paid from the tax refund.  You will receive the refund as stated on your tax return and you will need to pay the taxes owed as stated on your tax return.

This just happened to me. It says my state refund is $189, but then says on same page it’s less, which is minus exactly what I owed for Federal (but I paid Federal with credit card). Did you find the answer to why yours did the same thing?