You can't fix this on your own. If it is fixable at all (it may not be), you would have to get the IRA custodian to issue a corrected 1099-R. Even if you try reporting it on your tax return as a non-taxable correction, the fact that the 1099-R is coded as a regular distribution will mean that the IRS computers will automatically send you an assessment for taxes and penalties.
I believe you can reverse a contribution for any reason within the tax year, not just for excess contributions. You also have to withdraw the earnings on the excess contribution, because those earnings are taxable in the year the contribution was made. The problem is that, having made a regular withdrawal, this may be un-fixable, and you are stuck with the taxes and early withdrawal penalty.
