I'm not sure how satisfying the apologies will be, but here are some. It's pretty hard finding exactly what you want since for the most part the seme either barely apologizes or somehow the uke ends up apologizing instead even tho they were treated poorly.
http://www.mangago.zone/read-manga/koitomo_/ has a scene near the end where the seme apologizes for being mean while they're having sex, I don't really think they do much to make-up for it tho.
http://www.mangago.zone/read-manga/tamayura_yuki_ringo/ Personally I think this one fits your description, but maybe you won't agree? It has a good ending at least!
Same with this one http://www.mangago.zone/read-manga/hana_to_junketsu/
This too http://www.mangago.zone/read-manga/oko_sama_star/
Oh but the one's I gave you have the seme apologizing(?) or at least trying to make up for their actions
I was wondering if anyone could please suggest some yaoi where the seme actually feels bad for his mistreatment of the uke and apologises sincerely and tries to make up for it? I just read 'Kuzu de Baka ni wa Nido to Awanai' and 'Deep Flower' and now I'm just sitting here, all sorts of put out. Please help?