Employment Law Questions? Ask an Employment Lawyer.
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It doesn't. There is nothing in the law hat would require the filing of a complaint against you rather than the person that committed the act. I suspect whoever they are talking to at the EEOC just does not understand the facts.
People typically file a complaint against their supervisor when they have complained and their supervisor has refused to do anything about the issue, which is likely what the EEOC representative thinks happened. However, if you don't actually have the authority to do anything and have done everything you can then you would not be named in the charge filed other than as a witness.
You don't really have any recourse. The employee's recourse is to file the charge of discrimination accurately and see what the EEOC does. They usually (90%+) don't do anything and the employee ends up having to file a lawsuit. The EEOC documents can then come into evidence which is why it is important that they are accurate because if the employee claims you are the issue now and then claims something else in the lawsuit it is a sure way to lose.
The employee may consider hiring an employment lawyer to assist in filing the EEOC charge.