Solved
They didn't report my $3000 bonus as a separate payment, but I noticed that TurboTax has a separate option for bonus payments. Will this affect my taxes due?
No, this should have no effect on your taxable income. How this income is taxed depends on where in the income is reported on Form 1099-MISC.
In general, the income reported in Box 7 "NonEmployee Compensation" is considered self-employment (SE), which is subject to self-employment tax above your regular tax rate. If you received a bonus as a self-employed person, that amount would be included in SE income, regardless of how it was entered.
Income in Box 3 "Other Income" is generally not income from self-employment (and therefore not subject to self-employment tax).
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