On my susceptibility weighted imaging scan there were two small black spots. dr said these were just blood vessels. how can he know?

They probably: had a characteristic appearance that the doctor sees all the time, and were therefore of no significance.

Unable to answer: Unable to answer the question without further details; why did you have the imaging study? Context of the reported "black spots". Please provide more information. The imaging of venous blood with SWI is a blood-oxygen-level dependent (BOLD) technique which is why it was (and is sometimes still) referred to as BOLD venography. Due to its sensitivity to venous blood showing vessels as black.

Vessel vs old blood: Hello. If you are speaking to a brain MRI (susceptibility weighted), and the structure is dark and has a curvilinear path, it is likely a blood vessel. If there is focal blotch of darkness, that is likely the old evidence of some deposited IRON from HEME (the Oxygen carrying molecule of our blood). That deposit is likely evidence of an old bruise/capillary damage with some local blood leakage