Add your entire pretax income registered on each paycheck to get your annual income for the year for which you are filing income taxes.
Obtain your W-2 form from your employer in January or early February of the year following your earnings.
Compare the W-2 income to the aggregate income you earned for the year. The two should match.
Call your SEP IRA plan administrator to get the amount contributed on your behalf by your employer if your income and W-2 do not match. SEP contributions should not be included on a W-2 since it is not a salary-reduced contribution program, but it may have been an inadvertent mistake.
Contact your employer regarding any mistaken additions of the SEP contributions to your W-2. The assets should remain in your SEP, but your employer needs to issue an amended W-2 and record this with the IRS.