If my sons Pediatrition prescribed him vitamin D supplements does that count as a medical expense? Also if insurance pays for certain medication is that a medical expense

No. The medication that the insurance paid for and the vitamin D supplement are not deductible.

You can't deduct medication that your insurance paid for as medical expenses.

Medical care expenses must be primarily to alleviate or prevent a physical or mental disability or illness. They don't include expenses that are merely beneficial to general health, such as vitamins or a vacation.

Publication 502 (2021), Medical and Dental Expenses