Not only in yaoi but in all adult genres, like hentai, seinen, josei/adult shojo. The reason why rape and sexual harassment is common is because in real life is not different. fiction is inspired by real life. those stories are just showing how a great number of japanese men behaves in real life. check these links when you have time. articles explaining about the behavior of japanese men and one of the leading organizations fighting for womens rights in Asia, was created by a japanese woman.
http://www.nippon.com/en/currents/d00171/
http://www.ajwrc.org/english/sub/voice/21-1-2.pdf
https://apocketofwords.wordpress.com/2010/09/22/rape-in-japan/
http://www2.warwick.ac.uk/fac/cross_fac/iatl/reinvention/issues/volume1issue1/gray/
http://www.thejakartapost.com/news/2013/06/11/japan-s-immature-attitude-sexuality.html
http://www.ajwrc.org/eng/
Thanks for making this list. I'm tired of the rape in all adult mangas genres. To be honest I don't mind when rape is showed for what it is, a crime, a betrayal from the person the character loves, etc. But I really dislike the romanticize/rape=love, it's sickening. It will be always hotter to read about characters playing the game of seduction XD