I had the same problem. First thing I did was check online to verify my refund status. Turns out, the IRS recognized my mistake and adjusted the refund downward. I then went into form 1040-X and adjusted line 18 to reflect "Overpayment . . . as previously adjusted by the IRS."
Once I entered the revised refund amount, as determined by the IRS, TurboTax shows that I do not owe the IRS additional money. This is because the IRS now recognizes I am due a smaller refund.
I have held off e-filing my amended return until I receive the IRS adjusted refund.
