I have the exact same question and situation. Wife is retired, I am not yet retired. She had a small amount of capital gains exclusively hers, the rest are joint with me and marked accordingly in the federal return. TurboTax Georgia preallocated all of the capital gains to me except for those that are exclusively hers. When I divide the capital gains allocated to me in half (since all of mine were joint with her) and add them to her exclusive capital gains, our tax refund is reduced significantly (but not surprisingly). Like the original poster, having to do this manually seems wrong since all of the capital gains income were already marked "joint", "taxpayer", "spouse" in the federal return. I rechecked them.
