Malabsorption during teens/puberty can arrest overall growth—height, frame, body structure, gonadal development etc. Hence, a person may have less prominent frame—including facial frame.
However, if a small frame runs in families, then this can also be a contributing factor. Another possibility is vitamin D deficiency, or a bone disease. It would be best if you could get a doctor to examine you and see whether you need investigations. Take care!
So if your calcium absorption is not impaired and your nails are still growing then it is likely your body's bone should be developing properly? And the malabsorption would likely have to be pretty severe for growth to be affected?