Yes and no. Yes, violent stranger rape is a tiny percentage of rapes, but the communication thing is (according to a study by Lisak) largely a post-hoc rationalisation; at the time communication is actually quite clear, but because of this myth, pretending to misunderstand etc proves an effective form of plausible deniability. Alcohol, yes, definitely, as again it's just another cloak of plausible deniability and 'social license'.

I have seen studies as well. And written two college papers on the subject. And was raped -- by someone whom I am quite confident thought he had my permission...until I began screaming and crying. At which point, he got up and left, without ejaculating. I am confident he did not intend to hurt me. So my first-hand experience, as the victim, indicates that, at least some of the time, no, honest, it was a really terrible misunderstanding.