Something's got her upset. Scared, maybe, or worried? He's not sure. But somehow, seeing him here has upset her, and Joel can't abide that. He never wants Ellie to be upset with him.

He reaches out, to grip her shoulder, a comforting gesture, just to show her that he's really here.

"Hey, it's okay. The last thing I remember, was gettin' settled in Jackson. I was going to go out with Tommy in the mornin', start learning the patrol routes. I'm sorry if I worried you."

Maybe that's it - why she's upset. Did she think he left her?