"I received a notification from the IRS stating I under reported income and is referring to an amount that appears to be the overall value of the shares not the actual gain I realized."
It would be most helpful if you described exactly what the IRS said, but I'm guessing that a 1099-B (or 1099-Bs) was generated, (1099-Bs aren't required for a "same day" sale, but sometimes the broker creates them anyway), and you didn't enter it, or them?
This is a frequent error on the part of people who do same day sales of options as they reason that entering the 1099-B(s) would double their income and they know that can't be right. The problem here is that the 1099-B(s) don't show the correct basis to use when reporting the sale but they still need to be entered as sales in your income tax return with an adjustment to the reported basis. Most same day sales show a small loss due to selling commissions and fees.
If this isn't your issue then a fuller description of exactly what the IRS thinks your error is might elicit a helpful response.
