When Stefan comes to rescue her from Elena (it really pisses her off that she let the little bitch get the best of her), there is a small part of Katherine that thinks he's doing it for her sake. The rest of her assumes it's for Elena's sake, but eventually she realizes that it's actually because of the Bennett witch.
She sees the anger and hurt in his eyes when he realizes Elena would have been willing to kill her best friend even after finding out she and Bonnie were linked mystically.
She also sees the relief flow through him when he is finally able to convince Elena to let her go. Still she thanks him making sure to make her voice slightly sultry to screw with him a bit. She is not surprised by his less than enthused response nor is she shocked by his excuse for saving her.
She is however surprised when he quickly rushes back to Bonnie's side, checking for any injuries before pulling her into a tight hug. It's not so much that the sight of Stefan hugging the witch that is a shock it's that he barely spared her doppelganger a second glance after he convinced her to back down.
Despite the fact that her doppelganger has apparently fled scene, Katherine's curiosity is now piqued so she decides to stick around to observe what happens.
Katherine watches as Stefan hauls Bonnie into a frenzied kiss and it becomes clear that this not a first time occurrence based on Bonnie's enthusiastic response.
She wonders when their affair first started and why it even happened in the first place. In the past she might have reacted to this with some jealously, but now all she feels is a form admiration. Mostly because she knows they both (especially the witch) have a tendency to be selfless martyrs when it comes to Elena. It's something that actually disgusts her about them despite being on opposing sides with them most of time. With their power she knows they are capable of a lot of mayhem, but for some reason they feel the need to play superhero instead.
So to see them in the midst of a tryst with no regard for anyone but themselves actually makes them more interesting. A smirk appears on Katherine's face as she watches their kiss grow more passionate, making her wonder just how far they plan to take things. Her silent question is answered when Stefan lifts Bonnie into his arms before speeding away presumably to find them some privacy.
Katherine grins outright as she realizes the good that could come from this newest surprise. Katherine planned had planned on just killing Elena, but now she's thinking that she torture her before hand in order to make things more interesting. Elena finding out about Stefan and Bonnie would be a great way start.