Hi! It means that your face is showing some mood, mostly sadness. So if you are sad and your face shows it, or if you are tired, even if you are very happy, someone can say it to you. It's an expression when clearly you are feeling something and your face can't deny it. "Vaya" in this type of phrases is used as "qué" ("¡qué carita traes!"). We use it as an expression to talk about the quality of something, for example: "¡Vaya zapatos tienes!" = "¡Qué zapatos tienes!"

Your face is no good. And we use "vaya" like wow! Que carita traes