The 12,000 also increases your total income so it can and does increase your tax bill on your income even though the long-term capital gains themselves are taxed at 15%. As long as you have the records that show your basis in the stock for when you purchased it and you have entered that correctly then you should be good to go.
Here is a quick article on how to adjust your ESPP cost basis. If you have already done all of that you should be good to go.
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