Why do some people with autism have unusual facial features but others look normal?

Dysmorphism. Or unusual physical features are seen in many genetic disorders, some of which have intellectual disability &/or autism as part of their neurodevelopmental profile.
Not sure. I'm not sure what you mean; but since there is such great diversity of facial features among everyone, there really isn't any association between autism spectrum disorder (ASD) and "unusual" facial features. ASD is a neuro-developmental condition, and has no physical attributes associated with its particular pathology.