Your capital gains are not exactly taxed twice. There is income tax on the capital gains and the net investment income tax of 3.8% (calculated on form 8960). This tax is actually the Medicare contribution tax.
Please read this TurboTax article for more information:
https://turbotax.intuit.com/tax-tips/investments-and-taxes/what-is-form-8960-net-investment-income-t...
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