If you never applied for the extension, you are just late. You can't ask for an extension after the deadline. However, by itself, that will not cause a rejection. A rejection means something on your return doesn't pass the basic level of IRS quality check, maybe the spelling of a name, or a social security number, or a missing form. If you can't solve the problem by adjusting your return based on the error message, you will just have to print your return, sign it, and mail it in.
