Qualified dividends and long-term capital gains would always be a positive number as these represent sources of income. If your long term capital transactions results in overall losses, then those would not be reportable as income, just as capital gains would not be reported as losses.
Since it's hard to determine what is happening with your tax return online, you also have the option of using TurboTax Live for further assistance. An expert will be able to look at your return and help you resolve the error message you are receiving.
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