Use form 5329 to ask for forgiveness and then enter the distribution as normal in the year that it is actually taken.

Its way down at Part IX of Form 5329

And do NOT pay the penalty.... it's much easier for someone at the IRS to just 'forgive' than it is to find someone to write the refund check.

And in my experience, I've never seen a request denied.  Be sure to emphasize that the late distributions have been taken and the steps taken to make sure the oversight will NOT happen again.

Good luck