What are the causes of congenital anomalies besides bad genes?

Accidents. Early accidents in the cellular or molecular level can lead to birth defects even when the genetic make-up of the conceptus is normal. Examples: amniotic band sequence, previable rupture of membranes, in utero infections (e.g. Cmv, rubella, toxoplasmosis, herpes, syphilis, hiv), teratogens (heat, drugs, radiation, environmental toxins, alcohol), pregestational diabetes mellitus.