I always try to immediately turn the tables and ask why my T thinks whatever she's expressed, what her thoughts and feelings are. Like others have said, they're just her impressions and knowing why she has that "idea" can help me clear up any misunderstandings on her or my part.

I would tell her that you have been bothered the last couple of weeks about her statement that she doesn't think you're telling the truth about your use of the tool and just see where that takes the two of you.