Answer:
Marshall did not grant Marlbury his commission papers even if he personally felt they were deserved because the Supreme Court did not have powers to give it.
Though he wanted Marbury to get his commission and was positive for the court to give an issue order but Judiciary Act of 1789 had given the Supreme Court all the powers and rights to handle such issues.
Hence the Supreme Court could not force Jefferson and Madison to appoint Marbury, due to its lack of power.