That's like saying children of age 6 are overrepresented in kindergarten, because there is a higher proportion of kids of age 6 in kindergarten than in the total population!
The "natural" (equally-represented) proportion isn't that in the total population, it's the proportion in the population of interest, which in this case is the set of qualified applicants.
The meaning of words does depend on context of course. Regardless, rest assured that when you hear someone say "overrepresented" and they are talking about higher education, they are using the definition I gave you above.
