I received notice from the IRS that they are disallowing an amount I claimed as excess social security tax withheld because the amount I reported was based on both filers

[VolvoGirl]

That's right.  Is it for 2015?  (It's the same answer for 2016).

Are you married and filed Joint?  And you both had W2s?  The IRS is probably right.  They usually are in this case.  You assigned both spouse's W2 to the same person so it looked like that person went over the max.

Do you still have copies of all the W2s?  Look at box 4.  Did either of you have more than 1 employer?  You only get excess SS back if one person had more than 1 employer and those employers took out more than the max of  $7,347.00.  So add up your W2 box 4.  Is it more?  Then add up your spouse's W2 box 4.  Is their box 4 more than $7,347.00?

AND if you transferred from 2015 into 2016  the W2's will have transferred over wrong again so you might have the same problem.  For 2016 the max is $7,347.00.  So check and see if you have an Excess SS showing up on 1040 line 71 for 2016 or you will have the same problem.  
 
THEN for next  year, if you transfer over from 2016 you should delete ALL the W2s and re-enter them from scratch making sure to assign them to the right spouse.