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Rental property does not qualify for the VA capital gains exclusion. That is for the sale of certain small businesses. What "went wrong" was you answered yes (in the Turbotax interview) when asked if you qualified for this deduction.
If you disagree, The TurboTax (TT) accuracy guarantee process is explained here
but it only covers actual CALCULATION errors in the program, not user error (and it’s almost always user error), and it only pays any penalties or interest resulting from that error, not the taxes. Either way, you are still responsible for the increase in tax.
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