You are correct; employees here on H1B visas do indeed have Social Security and Medicare taxes withheld - see https://www.irs.gov/individuals/international-taxpayers/aliens-employed-in-the-us-social-security-ta...
This is (in my experience) usually an issue for students here on F-1 or J-1 visas.
OK, let's see how the IRS responds to you when you send them the follow-up.
