Run the End of Year Processing wizard for every year after the incorrect year up until the year you actually wish to run the wizard for, so that the wizard processes the graduating students correctly for each academic year.

For example, if you meant to run the wizard for 2013-2014, but ran it for 2011-2012, run this wizard first for 2012-2013, then 2013-2014. Make sure that on the Additional information tab of the wizard that you are marking the box to process graduating students.