The $600,050 applies to all of your income. So if your total taxable income with the sale of the home was greater than $600,050, then the amount above that would be taxed at the 20% rate instead of the 15% rate. The 20% rate only applies to the amount above $600,050. Below that it would be taxed at 15% and 0% according to the brackets.
If your MAGI is over $250,000, but your taxable income is below $600,050, then it is possible that you are seeing an effective tax rate on this of 18.8% instead of 20% due to the Net Investment Income tax of 3.8%. This is based on your Modified Adjusted Gross Income.
Was this home ever a rental? If so, then you may also be seeing a tax on the recapture of depreciation which is 25% for real estate.
Look at your Schedule D worksheet, Capital Gains and Qualified Dividends worksheet to see for sure how you are being taxed and the rates that are being applied.
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