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

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.

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.