Rly love this one. Also, first time I've seen the existence of homophobia addressed at all in a yuri manga.
Yuri Deadline opens with the high school MC running from home because of homophobia.
Green Tea Bitch: mother of one of the MCs is very homophobic.
Blue Star On That Day: nothing really explicit yet, but mentions of possible trouble, and side chars who'd probably say "gross" if they knew.
I Love The Villainess: Claire gets quickly called on a bit of homophobia; Rei's trans friend committed suicide due to transphobia.
Girl Friends: actually it's been too long so I'm not sure, but maybe?
A Face You Shouldn't Show: MC has been outed as WLW and it's destroying her career, and her partner is at risk too.
She Loves To Cook, She Loves To Eat
Moon On A Rainy Night
Ayaka is in Love with Hiroko!
How Do We Relationship?
My Dear Lass
When the Villainess Meets the Yandere
Li Zi and Nian Nian
Those are some other examples that I remember homophobia or least issues being accepted, fitting in, with friends and society, are things that come up. Though it's been a bit since I read some of those so I apologize if my memory is off at all.