Once you have filed your tax return as Married Filing Joint (MFJ), you cannot amend your filing status after the April 15th deadline. Any change to filing status has to be done before the deadline.
However, since your spouse did not agree to the Joint filing (did she file her own 2014 return?), I suggest you talk to her, and then call the IRS for guidance. You may have a hard time convincing the IRS that this was just a clerical error, since you would have had to electronically (or manually) sign your wife's name to the return.we have been separated for over 2 years
Did the same thing happen for the 2013 return?