http://www.mangago.zone/read-manga/shounen_no_kyoukai/
^ High school students who were previously his friends were thinking of raping him when they found out he was an omega. His childhood friend stepped in and unwillingly gave him a bite. It's a nature vs nurture story that focuses on fated pairs of the omegaverse.
http://www.mangago.zone/read-manga/romantic_joutou/
^ The omega got raped by an alpha but the endgame is beta/omega. One of the few mangas that actually show what happens when a bitten omega has sex with someone that isn't the "partner that bit him".
http://www.mangago.zone/read-manga/sayonara_koibito_mata_kite_tomodachi/
^ I think this might be what you're looking for. Never read it myself but I do know it's got gang rape.
Can anyone recommend me a lot of yaoi mangas where omega is being rape.