Your phrase is not correct. You can say:
- Hay matices cuando aprendes un idioma...
This is bit strange, anyway if we translate matiz=tone, the key in this phrase is:
There are tones when you learn, so the tones apear when (cuando) you learn.
-Hay matices en el aprendizaje de un idioma
More common, here the key is that in the process of learning (aprendizaje), there are tones