The presidential oath is not taken by the Vice President upon the 25th Amendment's incapacity provision being invoked. An Acting President is not the same as President. The former merely exercises the powers and duties of the President, without actually holding the office of President.
McNally recommends going to Threat Condition BRAVO. Due to the similarity with DEFCON, THREATCON was renamed to FPCON (Force Protection Condition) after the 9/11 attacks, two years before the story took place.
During commencement, President Bartlett marches out with the university's president. Guest speakers at commencement never march but are merely seated on stage. Only graduating students and university faculty but never the administration.
To demonstrate the young looking Secret Service agents' abilities, Agent Butterfield says "Attack Randy". Butterfield is not directing Randy to attack. This instruction is given to Wesley, who advances on Randy as if she were the person being protected. Upon advancing, Molly steps in and tosses Wesley "like a bag of potato chips," demonstrating to the President that they have the capacity for overwhelming force.