A heart murmur is heard when blood passes through an opening that makes it turbulent. Could be caused by defective valves (stenotic or prolapse/insufficient), holes that should be closed (atrial/ventricle septums), or unusual connections (patent ductus arteriosis).
It is not uncommon for newborns to have a patent ductus arteriosis (embryonic connection between aortic arch and pulmonary artery)--this could cause a murmur but is usually beningn and will close on its own or with indomethacin. Newborn could have patent foramen ovale
(between left and right atria)--this is also usually benign.
Other causes of heart murmurs in newborns:
1. Ventricular septal defect
2. congenital bicuspid aortic valve
3. tetralogy of fallot
, overiding aorta, ventricular septal defect, right ventricular hypertrophy
many many others......I can't remember without digging up books/notes.