Here are a few patterns I've observed:
pattern (a) MAN: does shitty thing; WOMAN: hey please stop; WOMAN's performance review: "has conflicts with MAN"
pattern (b) MAN: does shitty thing; WOMAN: reports shitty thing; MANAGER: oh MAN is a nice guy, why don't you try working it out yourself
pattern (c) MAN: does shitty thing; WOMAN: does nothing because she actually reports to MAN
> Oh… well then I should have applied for that internship.
A simple response like "what do you mean?" would be completely appropriate. Given the context of this example, I have a difficult time accepting the male was implying anything like what the author felt was directed at her. Rather I think it's a more reasonable assumption he came to the conclusion that if so many people from his school got Facebook internships, then he should have applied as well. But, we'll never know unless people do ask for a deeper explanation instead of just assuming malice.
Going with OP's examples, I would have said the same thing as the guy said concerning her even if it was a male.