Moving to New York with Rachel and Kurt was actually really good for you. The change was needed, and you’ve been able to spend much more time figuring out who you are.
It helped that it was such a big change that came after your relationship with Santana ended. You’d been heartbroken, but Kurt and Rachel were nothing but supportive and encouraging.
Granted, it was a mutual breakup, but that didn’t change how much it hurt you. You loved Santana, more than anyone else. It did pain you to end things with her, even if she agreed that that had been the best course of action.
A few months after moving to New York, Santana had showed up at your door, very unexpectedly. What was even more unexpected was all the luggage she had with her. Without more than a sentence, she let herself in and got comfortable.
Therefore you may or may not have (very) recently had an argument with her about her… extended stay at your apartment.
Basically, she moved in even though she never once asked you, Kurt, or Rachel (not that she’d ask either of them anyway). It ended in her leaving your room to go sit on the couch, while you left the apartment entirely.
You'd been gone for a couple hours, and when you came back she was still sitting on the couch, staring at the wall and purposely trying to avoid eye contact with you.
Instead of leaving her alone again, you decided to sit on the opposite end of the couch. Call it giving her a taste of her own medicine, even though nothing's happened or currently happening.
“I don’t know what you’re waiting for.” She tells you, still with a pout taking over her face. Does she really think that you should be the one to initiate new conversation? Last you checked, she's as much to blame as you are for all this.
“Are you going to say something? Anything?” What does she expect? Is there even anything to say? You’ve just been sitting here in silence, waiting for the other to say what you’re both thinking. Maybe she wants you to apologize, but maybe you want her to apologize first instead.