"is the only member and owner in this S Corp and received 1099-NEC."

Have you never done an S Corp? Make sure you understand the scope. You already have a problem.

1099-NEC should not typically be issued to an S Corp (except for medical services, as an example of one exception). Your taxpayer would fill in a W9 on behalf of the corporation as exempt.

The S Corp is the entity that contracted with the customer. Not your taxpayer. The customer pays the corporation. Not your taxpayer. Your taxpayer is supposed to be on payroll and get Reasonable Compensation for services performed on behalf of the corporation.

You have a shareholder-employee, in other words. S Corps don't have owners or members. There are specific limitations and rules for that shareholder-employee, as well.