The only way I can see that it would cause an issue, is when the IRS processes the return and the EIN entered does not match up with the SSN reported in the personal info section of the return. More than likely, the IRS will just fix it on their end and not bother you.
But where it could matter is this: Did you make any quarterly tax payments using your correct EIN instead of your SSN? If so, how did you make those payments? Via U.S. Mail, or online?
