There are no big problems here. If your rental property is a SMLLC and is not taxed as a corporation, its under your SSN all the same. Your SSN and EIN are one.
If you have a disregarded entity, everything goes on your 1040. The LLC's EIN doesn't get entered anywhere at all if we are talking about a rental property on Schedule E.
The IRS wants your SSN on tax documents, so you need to correct going forward. Those who pay you and are paid by you should get updated W9 forms. A SMLLC that is not taxed as a corporation should get tax docs with your SSN. The IRS issued this change a few years back to prevent "matching" confusion with single member LLCs.
Its not the end of the world if you have your EIN on some documents. The important part is that you declare the income and expenses correctly. If you had a 1099-MISC with an EIN, that would be a bigger "matching" issue. The IRS is unlikely to be terribly concerned over a deduction.
