I had an amniocentesis which was normal, but my baby appears to have a cleft palate on ultrasound. Why wasn't this detected on the amnio?
Amniocentesis examines the chromosomes and can only pick out abnormalities related to chromosome problems. What you're talking about is a structural defect, which is an abnormality of normal development. An ultrasound, however, can pick up structural abnormalities such as a cleft palate.
Medicines and infections could lead to such defects in otherwise normal babies who have a normal chromosomal analysis. It's the same as an amnio not being able to pick out a baby that will be large because the mother smokes. An amnio is not that type of test.