BLs:
http://www.mangago.zone/read-manga/new_york_new_york/ ("uke" ended up being traumatized to the point where he couldn't have penetrative sex anymore)
http://www.mangago.zone/read-manga/smells_like_green_spirit/ (attempted rape portrayed as something terrifying instead of being brushed over as usual)
http://www.mangago.zone/read-manga/acid_town/ (MC has a fear of father figures thanks to being r@ped growing up)
most of these are about the aftermath because i haven't seen too many that show rape as a bad thing as it's being done, unfortunately. a lot of it is glorified :(
I tried looking for some but I’m sorry if it isn’t what you’re looking for.
http://www.mangago.zone/read-manga/oni_wa_warau_ka/ (They’re still children, there’s not much that they can do.)
examples
http://www.mangago.zone/read-manga/ore_higaisha/nbt/c004/pg-1/
http://www.mangago.zone/read-manga/aquaman/
http://www.mangago.zone/read-manga/dansei_kyoufushou_datta_watashi_ga_av_jouyu_ni_naru_made_no_hanashi/