When you sell ESPP stock, it is possible that you will owe both ordinary income tax as well as capital gains tax.  This TurboTax help topic explains:

https://turbotax.intuit.com/tax-tips/investments-and-taxes/employee-stock-purchase-plans/L8NgMFpFX

You shouldn't be taxed twice on the same dollars, though.    For example, suppose the share price of ABC Corp is $100, and you acquire a share at a discount price of $80.   Later you sell the share for $110.  You have $20 of taxable compensation from working, and a $10 capital gain.  That's normal.  You should not be taxed on $30 of capital gains on top of paying the tax on $20 of compensation.  If you think that is what happened, we will need some more details to help you figure out what happened. 

Did the sale show up on the W-2 and the again on the 1099-B from the broker in the same tax year ?    If so you need to adjust the cost basis on the 1099-B to reflect the taxes paid on the W-2.  Your employer should have provided the cost basis for you if the broker doesn't have the correct information.  Usually the 1099-B will show a loss in the amount of the broker's fee if it is done correctly.