If your wife did the consulting through the LLC and the income has been reported by the LLC, then the form 1099-NEC should have been issued to the LLC and there would not be any double reporting of income. You should have submitted a form W-9 to your client in the name of the LLC. You can ask your client to correct the form 1099-NEC to make it out to the LLC.
Please note that if you live in a Community property state (Arizona, California, Idaho, Louisiana, Nevada, New Mexico, Texas, Washington and Wisconsin) your husband-wife LLC is a disregarded entity and you could report its income and expenses on your personal joint return on Schedule C..
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