The fact that he's not an ally (this happened after War Games) and he's an armed man defying her orders.
Bringing up what she knows doesn't help your case. Because while she knows he's helped out, she would also know that he's had training equal to most Special Forces, she would know that he's got methods of rendering her gun useless (one smoke pellet and she can't fire), she would know that he has a history of resisting arrest, she would know that he's too dangerous to approach by herself, etc.