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In the U.S. the difference between employees and independent contractors (who are paid through 1099s) is that while an employer pays taxes for an employee an employer does not pay taxes for an independent contractors and independent contractors are liable to pay for all of their iincome taxes, employment taxes, etc. Whether or not an employer properly classifies a person, correctly, as an independent contractor or an employee is a matter that is not set in stone but one that is left up to a series of detrminations regarding how much control over the work and the person the employer has, the more control over how work is done, how the person works, etc. the more likely norjmally that the person will be considered an employee). This page here allows employers to determine who can be classified as an independent contractor or an employee. If an employer fails to properly classify an employee as an employee then they may be liable for employment taxes to the IRS/state (this is also discussed in the link provided above) if they did not have a reasonable basis for mistaking the person as an independent contractor.
The information I provided allows you to work through whether your classification error was one that was "reasonably" made, which is the distinction used to see whether an employer who misclassifies an employee would be liable for their salary wages. Also, an employer can also file a form with the IRS to have the IRS determine if they need to pay for the employee taxes for someone who was misclassified (the information on the forms and process to do this are also on that link I provided).
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