Simple IRA funds not removed from account

SUGGESTED

I have someone who has been contributing to a simple IRA account for a couple of years now.  She is paid bi-weekly.  I just noticed for the first payroll in January, SAGE deducted the companie's contribution to the Simple IRA, but not the employees.  For the 2nd paycheck in January, it deducted both as it should.  Have never seen this happen.  Not sure what caused this, but how can I rectify this situation?