Maekawa (Moka-chan) likes the manager. But this being a romcom manga she can't just come out and say it because that would be too direct. So instead she drops a ton of hints by talking about how he would be her type because he's cool and tall and "a proper man."
But he misinterprets it as friendly cheering up and imparting confidence so when he thanks her for what he thinks is a platonic gesture she gets annoyed and pouts as she leaves. He has no idea what he did to make her upset but the other two clearly do.
A trope can still exist even if it's something that occurs in real life. It's just a common trait in a story or character which writers and critics have identified to belong to a certain kind of story or writing.