My employer pays my health insurance premiums and gave me a 1099
I am assuming this is *NOT* an employer sponsored plan. That means the employer is just reimbursing you for the cost of the plan "outside" of an employer sponsored plan. If my assumption is correct, then your employer is flat out wrong to report those reimbursements to you on anything other than your W-2.
But how things are treated tax-wise depends on specifics not provided anywhere in this thread. I suggest you read through the IRS FAQs at https://www.irs.gov/pub/irs-utl/health_reimbursement_arrangements_faqs.pdf It covers the many different kinds of reimbursement plans in what I perceive as "plain language" that I can better understand and comprehend.
