You may have to leave the U.S., refile another way, or face possible deportation. The I-751 'usually' must be filed and accepted by USCIS 'within' the 90 day period before the card expires. There are very very limited exceptions. I strongly recommend an appointment with an experienced immigration attorney in order to decide the best action.
At times, there 'may' be limited options, but the details should be carefully discussed to avoid confusion and possible deportation.
The above is general information, not legal advice, and does not create an attorney client relationship.
Usually if someone files the I-751 late, the petition is denied. But if you have a good resaon for filing it late, explain the reason, and specifically request that the USCIS accept the late-filed petition based on your good reasons, then the USCIS may accept the I-751 and proceed to decide it on its merits. If the USCIS does not accept it, then it will place you in immigration court removal proceedings. The normal filing period is within the 90 days before your conditional green card expires.
I agree with the answers posted above. However, I once had a case where the joint petitioners came to me shortly after the 90 day period. We sent in the I-751 as quickly as possible but it was returned as untimely filed--similar to the facts in your case. I simply sent it in again, and it was accepted for processing. With the I-751, if it is accepted after the 90 day filing period, it is generally determined to have been timely filed. You might try this. It will not surprise you that the Immigration Service is not always consistent in how it applies its own rules. I also suggest, as the attorneys above, that you utilize the services of an experienced immigration attorney.