If you set up a payment through Turbotax, that information was passed on to the IRS or the state. Turbotax doesn't have your money and can't make the IRS issue a refund if you paid twice. If you only set up payment in Turbotax, but the IRS took 2 payments, that would be unusual, but also an IRS mistake, and Turbotax still doesn't have your money and can't make the IRS issue a refund.
You can verify that the IRS did receive 2 payments by checking your Account Transcript here.
https://www.irs.gov/individuals/get-transcript
However, it may take 4 weeks for recent account activity to show up on your transcript.
If it is more than 4 weeks since the second payment, and both payments are still not listed on your account transcript, you can contact the taxpayer advocate service to initiate a trace of the payments and make sure that both payments are credited to your account. The TDD number for the IRS is 800-829-4059.
Once both payments are registered as showing on your account, the IRS will recognize that you overpaid, and will refund the extra payment. This may take a few more weeks.
