The answer has nothing to do with their cause, however, but with the simple fact that dictionaries are not exercises in bi-unique substitutability; in other words, if one of the senses of run is `operate' (as in She runs an engine factory ), that does not make it valid to assume that one can substitute operate for run in We run in the marathon every year .  Although recognizing this as a shortcoming of dictionaries and assigning it arbitrarily to what, for lack of a better term, we might call the  genius  of the language, might seem trivial to the casual observer, it is a valid matter for concern in the realm of lexicology.
Although one can assume that one can substitute operate for run in "We run in the marathon every year", many people do not