There is a bug for some clergy customers, the selection to pay tax on both housing allowance and wages doesn't "stick" and the program calculates the wrong tax.

Some people have reported success by deleting the W-2 and starting over.

Until there is a confirmed online fix, the only sure way to stop this from happening is to change from online to the desktop program installed on your own computer from a CD or download.  Desktop does not seem to have the error and even if it did, you could fix it by directly editing the correct forms.  The desktop product is also more cost effective for most users, especially if you buy from a discount retailer like Staples or Amazon.

I have reported this several times, no word on any time frame for a potential fix.