Koko apologizing for not being able to give Jonah her opinion when he talks about how he still loves the world despite the awful things he's experienced.
Koko comforts Valmet after she kills Chan by telling her that she was able to avenge the deaths of her Finnish Rapid Deployment Force subordinates, putting their souls at ease and giving them closure.
Dr. Miami's recruitment of [Karen is this as well as funny; the good doctor sees a woman who tried to kidnap her (probably within the last year) huddled up on the street with nowhere to go after a mental breakdown. Her immediate reaction? She trots over and starts chattering at her, along the way offering a bath, a place to stay, and a job without a single hint of ill will toward her former would-be captor.
Valmet comforting Koko after R's death.
When Kasper's team hears about R's death, they all give a toast to him in respect.
The temper tantrum Chequita throws when Jonah leaves Kaspar's team shows she really liked him a lot.
The team and Koko welcoming back Jonah like friends even when Jonah drew out his sidearm and threatened Koko with it.