As long as you filed your return before the 4/15 deadline, it will not be considered late.  The status of your return will notify you when it was accepted or rejected by the state.  Even if the status is not updated until after the deadline, the filing date will be recorded and used to ensure your filing is timely.  

In the event your return is rejected, you will also have time to fix the error and update before resubmitting.  In that case, it will also not be considered as a late filing.