If the total amount of your mortgage balance exceeds $750,000, then the amount of your mortgage interest might be limited and could result in the error message.
Mortgage interest deduction limits
You can review your mortgage interest in the federal section of the program.
Since you just refinanced the same loan and if your total loan balance did not exceed $750,000 throughout the year, you will need to review your input.
Be sure that you have entered $0 for the loan that was paid off in Box 2 - Outstanding mortgage principal on the screen titled Let's get the details from your Home loan 1098.
You will also want to select that the loan that was refinanced and is no longer there at the end of the year is marked as paid off during the year.
Please see the following link for additional information on entering the refinanced mortgage interest expense.