No worries.  If you found that you have made a mistake on filing your return or if the CPA has omitted information simply complete Form 1040X. Make sure to provide an explanation for the mistake. The IRS will contact you concerning the submission and review the amended return. The IRS could ask for additional information or simply process the amended return and either issue a refund or accept payment. Form 1040X is a paper filed form. The IRS could take sometime in processing the form so be patient. You could also have to file an amended state return. In most cases I recommend working with a CPA. A client does not want to get in a position were they are filing a corrected Form 1040X.

Generally, to claim a refund, you must file Form 1040X within 3 years after the date you filed your original return or within 2 years after the date you paid the tax, whichever is later. Returns filed before the due date (without regard to extensions) are considered filed on the due date.