That can happen the last week of the filing period, as a gazillion state tax returns get dumped in at once. That and unusual CA computer system overload/crashes with teh mass of files going in, could affect the system giving you a final response.
The Filing date is based on when it was filed...not when it was finally accepted by the state.
The only issue you might have is if it gets rejected by the state...and you have to correct something and re-e-file. The feds give a 5-day grace for file submitted on-time...but rejected. Not sure what CA does for that situation.