When Kaeloo gets angry during her trial, the way Mr. Cat tries to calm her down looks more like an attempt to console a sad person than an attempt to restrain an angry one. Mr. Cat tends to mask his feelings of sadness with anger, and when you consider the fact that Kaeloo has just been betrayed by Stumpy and Quack Quack and called a "criminal" by one of her own beloved flowers, it's likely that Mr. Cat assumed that Kaeloo's anger was just a way for her to cope with her sadness.
Mr. Cat takes Kaeloo's side because he's too smart to be manipulated by the aliens, and he's a manipulator himself so he can recognize the signs of manipulation.
Mr. Cat tries to placate Kaeloo with physical gestures rather than words because it's worked twicebefore.
Mr. Cat explains that he was late because he slept through his alarm so he had to be dropped off by his parents in their car. His parents. The show's Negative Continuity has screwed up so badly that in this episode, Mr. Cat still lives with the Cat family.
