I made a nondeductible contribution but paid taxes on it. I didn’t remove the $ from the IRA. As I paid taxes on the contribution, do I have excess contributions?

In 2012, I made an IRA contribution of $6,000.  I deducted the IRA from my 2011 taxes.  In 2012, I received notification from the IRS that I owed taxes on the $6,000 because I also had a 401K.  I amended my 2011 taxes and paid the taxes on the $6,000 to both Federal and to state.  I did not remove the $6,000 from the IRA (I didn't know to do so).  As I paid tax on the contribution, do I have excess contributions?