She has, in fact, been out for a run...and when she sees Scott, her body responds for her.
Her features melt into a warm, sunny smile of recognition, her hand starts to lift in a wave--and then she realizes and stops what she's doing.
Because it's Scott. And not only has she been avoiding him because of random elevator sex...but she still can't bring herself to talk to anyone about the stuff that came out of her mouth when she was wailing on Stiles.
She's stuck, however, so as she lowers her hand again, she finishes jogging up to the door, still smiling, only now with a look in her eyes that's somewhere between affection and a frightened animal preparing to run at any moment.