"He indicated to me that the medical insurance premiums paid for his coverage are not included in his W2 income."

Just how wrong did the employer get it? Who prepared the 1120S? They should have checked for this provision.

"However, in the additional information it states "medical insurance premiums for more than 2% shareholders" is $9k"

Do you see it as part of Box 1, or not? You mention "the additional info" but what is that from?

Have you talked to that S Corp provider, or the payroll person? They can make late amended/corrected filings.

Here are nice references to email to them; the second one has nice imagery:

https://www.irs.gov/businesses/small-businesses-self-employed/s-corporation-compensation-and-medical...

https://www.rmncpas.com/~rmncpas2/files/S%20corp%20health%20insurance%20rules.pdf