If you e-file that return then the IRS is going to expect the amount shown on Line 50 to be the amount to be paid. There is something else going on here because if TurboTax does nothing else it is great at calculations. This would not be a systemic issue because we would have seen this problem on the forum multiple times and this is the first.
Suggest you contact TurboTax support through the Contact link at the top right of the program screen. Click on Contact and click on Contact Us. Post your problem, something like "Form 1040A calculation error on Line 50" and then click on Call Us.
