This is a reference to the Munich Agreement made in 1938 between Germany, France, the United Kingdom, and Italy. It allowed Germany the annexation of portions of Czechoslovakia and is nowadays largely considered an act of inappropriate appeasement toward Germany, encouraging it to proceed with its agressive politics. JFK's father Joseph Patrick Kennedy was US ambassador in Britain at the time and a supporter of Britain's appeasement politics.
Its relevance to the Cuban Missile Crisis (though, I haven't seen the movie Thirteen Days in particular) is, that the moral of the Munich Agreement can be seen as being that
appeasement discredits the defenders' willingness to fight, and encourages the aggressor to escalate his demands.
They are thus afraid it might come to a repetition of the "Munich Lesson" if JFK stays too inactive during the crisis, encouraging the Soviets to take more severe steps, especially since his father already was a facilitator in the original Munich Agreement.