Employment Law Questions? Ask an Employment Lawyer.
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If you are an independent contractor, your rights are limited to whatever is stated in your contract and by what rights the law generally confers on the parties of a contract. Generally, it would be illegal to take out money from a contractor's check unless the contractor consented or the parties' agreement specifically allowed for such a deduction. In all other circumstances, the employer would need to go through the court system rather than simply offsetting what they "believed" they were owed.
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Small claims court would be one option. But very often independent contractors are misclassified as such and should actually be employees. If you should be classified as an employee, then the deduction from your wages is illegal and you can file a wage claim, which is an easier (and free) process compared to a lawsuit.
You can read about the distinction between contractors and employees here. It's not up to your employer to decide how you are classified, it's a function of your job duties. If you think you can argue that you should be an employee, filing a wage claim may be much easier than a lawsuit in small claims court.
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