What're the causes of congenital anomalies?

Multifactorial. Genetic, environmental, infectious, metabolic reasons or even developmental accidents can cause birth defects. Taking Folic Acid at 1-5 mg daily throughout your reproductive life could prevent 95% of neural tube defects and up to 75% of cardiac defects.
Multifactorial. Depending on which disorder, causes include genetics, maternal alcohol or drug use, vitamin insufficiency, idiopathic, etc.