What is a congenital deformity or malformation?

Abnormal birth. Any abnormality in the baby is considered a malformation. It can be as simple as an extra digit or as severe as multiple malformation syndromes that can be lethal to the newborn.
Terminology issue. Malformation implys that the tissue or organ involved did not follow the normal pattern, like a cleft lip or palate, or heart defect. Deformity implies the distortion of normal tissue/features by an external event. Abnormally shaped feet, legs, facial features, etc due to the fetal position in the womb, are examples.