Yuffie was surprised to see him considering their last confrontation. It's safe to assume that she had been avoiding him. She was the one who usually visited him at his shop and while it was fun, Yuffie never did tell him where she hung out before that. Which meant that avoiding him was easy.

"Figured you'd be here to lock your folder."

Her tone was tense and she kept a distance between her and MarKus. She really didn't know how to handle this sort of thing.