That is so gutting for you - sorry, I feel your pain. :( I think that in any applications you should always highlight the actual percentage that you got - e.g., in personal statements/cover letters/emails. This could help. Additionally, if you have relevant experience and other things (obviously you did get higher grades in other modules) to boost your application I don't think it is the end of the world in terms of PhD applications. I'd say try to talk to a few different academics in your institution to get more advice. You never know. Good luck.