http://www.mangago.zone/read-manga/escape_journey/
I think there is scene similar to your description... sort of.
Little Spoiler -> Seme hurts uke a little bit more, but it looks kinda "unintentionally", so I hope it's okay
http://www.mangago.zone/read-manga/yumemiru_otokonoko/mf/v01/c002/19/
http://www.mangago.zone/read-manga/kizoku_no_aoi_kuchizuke/tr/47976/page/97/
Welp I'd say the relationship was a game to the seme...then they separate...and seme regretted it and so on...happy ending though
http://www.mangago.zone/read-manga/zutto_issho_ni_kurashimashou/sa/sa-v1c001/30/
the entire manga is about the 5 brothers and their love life...they get happy ending
http://www.mangago.zone/read-manga/koishite_daddy/tr/145990/page/32/
http://www.mangago.zone/read-manga/zenbu_ore_no_mono/mf/v01/c001/21/
didn't really have those eyes but him apologizing..</3
http://www.mangago.zone/read-manga/myuzu_no_gakuen_de_aou/bt/203481/Vol2_Ch1/33/
well depends on perspective, if it was intentional or not.
http://www.mangago.zone/read-manga/junjou_romantica/mf/v03/c001/77/
well this is the seme but his expression ;w;
All of these have happy ending~ well the last one is still on going. Hope this help somewhat.
The ones from this page http://www.mangago.zone/home/mangalist/72632/?filter=&page=2 i got an individual review of each. Actually, you can read the whole thing, the list is a world of hurt and feels lol.
Can anyone recommend to me any yaoi where the seme unintentionally hurts the uke or there was some kind of misunderstanding and (p.s. this is the situation I'm really looking for), the uke show this super hurt-like eyes that tugs your heart from seeing the scene and the seme sees him like that... please make it a happy ending. Thank you (^^)