My recommendation is to amend your tax return. Theoretically, you don't need to amend your return if it doesn't change your refund/tax liability. Practically, however - the IRS has a copy of the 1099-MISC and will be looking for it on your tax return; they also don't know that you have expenses against that income. To avoid a CP2000 letter asking your for tax due on the $3000 and missing form, amend the return to show that you report the income and claim the expenses against it.
