Yes, your son should speak with the farmer and ask why the farmer is reporting his income as an independent contractor on Form 1099-NEC vs reporting his income on Form W-2 as an employee.
If your son is an employee than his employer, the farmer, is responsible for withholding employment taxes from your son wages and your son will receive a W-2 for his income working for the farmer
The general rule is that an individual is an independent contractor if the payer, farmer in your son's case, has the right to control or direct only the result of the work, not what will be done and how it will be done. Ref: IRS Understanding Employee vs. Contractor Designation
@MWolfe00
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