Actually, I just checked the website. You're almost certainly fine.
"You must register three referees as part of your graduate application. However, you need only two references submitted in time for the application deadline to be considered ready for assessment, as long as your application is otherwise complete.
You are still encouraged to obtain a third reference as early as possible, so that it can be taken into consideration when your application is assessed. The academic department assessing your application may ask you to have a third reference submitted before making a final decision"