The company that sent you the 1099-DIV has no way of knowing if you will owe tax on the capital gains, so its omission is not what that means.
It sounds like you have a 1099-DIV that is a sort of 1099-Combo, that is, it reports interest, dividends, and capital gains in various statements following the first page.
You should go through the various pages looking for these items, and enter them into your 1099-DIV interview in the appropriate places.
And you should call the agency that sent you this form and ask them why they did not include your capital gains in box 2a when you believe that the detail shows that you had them.