I received IRS letter CP11, saying that they changed my total premium tax credit because of incorrect calculations. I sent in Form 8962 but they still say I owe.

Ok... Did you send the 1095-a plus the 8962 when the IRS sent you a letter asking for these? If so did you have to go back into the program to add the 1095-a? If so did you happen to look at the newly generated form 1040 and how the addition of the 1095-a info changed the bottom line? If you did not look at it then save a PDF and look at it now.

When you sent in the 1095a and 8962 the IRS recalculated your return the same way you just did in the TurboTax system. So your refund did change and it should match the same refund as in the TurboTax program.

This is not a TurboTax error simply The logical result of adding the 1095-a form.