The biggest problem for prosecution is that it is more than most other crimes completely reliant on he says she says.
Very well, in that case:
Well, one big sexism that happens in rape cases is that many things a woman does to a man without anyone raising a legal eyebrow would be very different the other way around.
WWYD shows interesting cases were women doing stuff to men is way less reported than the other way around, one of this was sexual harrasment at work.
So "rape" being something men do to women (or to other men) is an important part of how rape is seen in culture.
For example, there was a movie about killing bosses were the female dentist raped her assistent. This was seen as comedy. While everybody wanted to kill the dentist in the audience ( though surely many men wanted to have sex with her first
) the movie would have changed of tone completely if the genders were inversed.
So yeah, there is sexism in the way we see rape.