This should not be an issue for the IRS. Although business owners should not issue themselves 1099s (while they are owners), this shouldn't cause any problems with your return being e-filed or accepted by the IRS. Just keep your documentation to show the IRS if they ever question it. You have done things correctly, no need to be concerned. I have seen business owners erroneously issue themselves a 1099-MISC and the IRS did not reject it or question it. There is nowhere to notate this on your tax return and trying to add an explanation somewhere could cause the return to reject.
