Either Kate's undercover or genuinely trying to progress in her new job, so I'd reckon whichever it is, she doesn't want to question her new boss overtly just yet.
I agree with what you've said that she didn't seem comfortable.
Possibly Jo is doing a bad job on purpose where she can, to offset the damage caused by what whomever is blackmailing her is forcing her to do. I.e. she had to delay the raid and is expected to get Terry charged but by doing such a bad job at it, she's got him released.
OR that was the ploy all along - make such a bad job of it that he's released to the unsafe safe house, and so he can't spill any beans to the police. Actually I think this is the more likely.
Not sure if that makes any sense for Kate or Jo - I'm confusing myself!