In early American history, such as with President James Madison, there were points in time when the vice presidency was vacant. That also happened with the assassination of John F. Kennedy; when Lyndon B. Johnson became president, his former post was vacant for some time.
(Fun fact: The vice president and president didn't always run as a ticket. In fact, the VP used to just be the runner up of the presidential election.)
In other stretches of history, a single president had multiple vice presidents throughout his time in office. Franklin D. Roosevelt alone had three vice presidents: John Garner, Henry Wallace and Harry Truman.
Because the two roles haven't always been elected or ruled in lockstep, there just isn't the same number of presidents and vice presidents. It happens to total up to 46 presidents and 49 vice presidents so far.