Can I file an amended return for 2014 from MFJ to MFS as it was filed in error by my wife and we have been separated for over 2 years and have not lived together.

Did you sign the return (either physically or electronically)?
Is your income on the tax return?

More importantly, did you and your wife agree to file a Joint return?  Normally, you cannot amend to MFS once you file MFJ.

No

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.

Did the same thing happen for the 2013 return?

The fact that you did not timely file your own, Married Filing Separately, return, infers consent to the filing of the  MFJ return. You'll have a hard time changing it now.