Are there any suggestions about yaoi manga where the uke think about being used as a replacement/substitute for someone else by the seme? But it's just misunderstanding.

The best example: Lover's Position by Minase Masara and Renai Kyoutei Nukegake Nashi! by Sakuragi Yaya

Sorry, if my english was bad. Thanks before.

Well, there's Caged by Love Shackled by Honey, but in my honest opinion, it' more smut than plot.
There's also Junjo Romantica (although I'm pretty sure you already know it and it's only like the first 2 chapters or so).
There are some other yaoi mangas like that, but it's the seme that's misunderstanding. If you're interested, there's Ikumen Datte Koishimasu and Kimi Ga Koi Ni Ochiru.
And that's all I could think of off the top of my head.

Yes, i've already read JR. It's okay, i'll try it all. Also, thanks a lot for your recommendation.

Hmm, maybe Kasa no Shita, Futari?

Sadly, i've already read that.

Onozomi No Mama Ni (ch5)

Empty Heart