The Machine doesn't miss anything. It knows what John needs even if he doesn't, sees how he watches Harold. And so it tells Harold what to do to John, where to touch him, what to say, and how to reassure John when he really isn't sure about this.

I just want the Machine and Finch topping the hell out of an unconvinced Reese, but he needs the reassurance all the same of being so looked after.

And the Machine knows this will just further bind John to Harold, to both of them.