Since the IRS didn't catch your mistake during processing, you should:

• File an amended return using Form 1040-X, Amended U.S. Individual Income Tax Return as soon as possible.
• Include any forms and/or schedules that you're changing and/or didn't include with the original return.
• If you received a check, return it with a letter of explanation. Write "Void" in the endorsement section of the check when you return it. Don't staple, bend, or paper clip the check. Allow 6 weeks for the returned refund check to be credited back to your account.
• Pay the tax due by the due date to avoid penalties and interest. If you file the amended return after the due date, don't include any interest or penalties as the IRS will make any needed adjustments. See the Instructions for Form 1040-X for payment options. 
• When your amended return has completed processing, the IRS will issue a new refund or a balance due notice.
• Allow up to 16 weeks for your amended return to be processed; see Where’s My Amended Return? to check your status.