retirement assets

Our financial adviser back in 2007 placed my wife's retirement account in the wrong IRA. It was supposed to be a Roth but was made a Traditional. For a span of 6 to 7 years, we were funding that account with after-tax dollars from our checking account. Now we are going to be taxed on that money twice, going in and coming out. How can we fix that issue, or is it too late?