Given that there is another employee, re-designating the excess to be an employer contribution might not be viable. If made as a profit-sharing contribution, employer contributions must generally be the same percentage of compensation for both employees. In your case, though, the employer contribution for you would be limited by compensation. Since the employer contribution on your behalf would be 10.88% of compensation, so the employer contribution on behalf of the other employee would have to be at least 10.88% of that employee's contribution unless limited by total additions of 100% of their compensation or because the employer contribution is defined in the plan to be a matching contribution and are instead limited by the amount the other employee deferred (but I think the plan would have to have already stated the terms for the matching contribution at the beginning of the plan year).
All of the deposits should have been made from an account of the S corp, either as the employee contribution from a portion of your compensation that was not included in your paycheck (the same as tax withholding) or as the employer profit-sharing or matching contributions. Since the deposit improperly came from your personal account, yes, the S corp would need to reimburse you since employer contributions are an expense of the employer and do not come from your compensation.
