The Supreme Court had no power to ensure the appointment of the last judges because the law that allowed citizens to bring a case directly to the Supreme Court was ruled unconstitutional.
In this case, William Marbury brought his case directly to the Supreme Court which is extremely unusual. However, at the time it was legal to take this action as long as it dealt with a "writ of mandamus". This phrase means that a court can demand an action from a government official.
Though it was legal at the time, the Supreme Court ruled that this law made by Congress was unconstitutional, leaving them powerless in helping William Marbury.