There has to be a time, surely, when Wei Wuxian returns inside. Just some before the train starts its leave, but it's coming to that close - and Tidus spots the older man then, with a curious look. It's not any of Tidus's business about who goes, who stays; he certainly won't think less of anyone for either choice.

But he can't help but to say, the question implied, without any further prompt than that visual:

"You're staying?"

He has more reason to think Wuxian would leave than stay, even if it's a vague one in his mind.