Some of the yuri-specific ones I mostly dislike but they’re so ingrained as to be like annoying old friends: such as: “But we’re both girls!”
^ This.
I am for some reason partial to a couple of old chestnuts: “She’s so close—her lashes are so long!”
I see what you did there. (I know, there are so many more examples...)
Romance in general, echoing Nevri: misunderstandings that only happen because the person’s blurted-out explanation needs one more sentence, or just a specific noun or two, so instead of just, “It’s not what it looks like!” add: “She’s my sister!” or “My brother’s girlfriend!” or whatever. Also hate: the other person running away before the explanation is complete.
"Lack of communication"/"Miscommunication" is a huge driving factor in romantic dramas in general, and I don't mind if those things are cleared up "in due time". Bloom Into You did that right IMO, because aside from major plot and character development hangups people actually talked to each other and resolved (or at least addressed) most of the conflicts within a chapter or two.
How Do We Relationship? / So, Do You Want To Go Out, Or? kept on dragging this aspect out endlessly, to the point where, despite the fantastic SAD translation, reading it felt a bit like a chore and I'm not even all that mad that they probably dropped it. The first 31 chapters at least felt more like How not to relationship than "How do we relationship".
It may not really be Yuri-specific but "conveniently inconvenient events" can also get old. Can't Defy The Lonely Girl kinda took that one farther than it should have.
Probably more associated with Yuri and also well exemplified in Can't Defy The Lonely Girl is sudden parental intervention after long periods of disinterest and/or neglect. Poof, Mom's arrived to ruin our lovely confession.