There is a penalty for late filing of an S corporation return even if no tax is due. I suggest you call the IRS at the number on the notice they sent you. If necessary, write a letter and explain what happened and include a copy of the notice you received showing you submitted it on time and was not aware it had been rejected. The IRS is often lenient when you have a good excuse.
Also, if you have a good history of timely tax filings, you can apply for first time penalty forgiveness. This may apply if you didn't have any tax penalties during the previous three years. Here is some information on that: IRS 1st Time Penalty Abatement
You can also file form 843 Claim for Refund and Request for Abatement Form 843
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