About a third of the way through The Bourne Supremacy Jason visits the only other living member of Treadstone in order to get information about Landy and other recently learned information (for example, him supposedly killing a couple of highly trained officers).
It was just established and implicitly agreed upon that Jason wasn't there to kill the man, and that the man had phoned in Jason being there. They were talking about Jason leaving and the man informed Jason that he had a second car out back that Jason could use, yet the instant moment the phone rang he attacked Jason (and even while in plastic cuffs!).
So, what's the reasoning behind him attacking/trying to kill Jason if Treadstone had been completely squashed/hushed at that point and Jason was just about to leave the man alone?