Sounding as if there is something off in the Form 1099-B entry since TurboTax is asking you to confirm the wrong amount of compensation income. Go back through the 1099-B entry in TurboTax and make sure that the form and your entry is reflecting only the shares that were sold to cover the income taxes. The 1099-B should only report shares that were actually sold, not the ones that were vested. Everything vested go to compensation income, but capital gains/loss only come into play once shares are sold or disposed of.
What are restricted stock units (RSUs) and how do I report them?
You can edit the compensation worksheet if you need to, see this answer to another multi-lot ESPP transaction.
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