In Cost of Two Hands, Adele and Cry of the Storm (a horse) do not get along. Adele loves machines and isn’t really comfortable riding something with a mind of its own. Plus, there is the small matter of Cry of the Storm trying to kill her because she is going to put Jonah’s soul in a machine. Just a minor conflict.
In the Sparrow and the Star, Jonah sends Cid on a mission with a rather unsavory person. (I’m not naming names because I don’t want to SPOIL it.) Poor Cid must put up with this person when they both mutually hate one another: he’s too dirty and untrained, Cid’s too clean and prepared. Ultimately, their conflict is Jonah. They both owe him their lives. They both love him, so they want to do right by him, but they’re unsure of each other.