The events of X-Men: Days of Future Past essentially wiped The Wolverine from continuity, but one part remained, and that's the fact that Yukio predicted the clawed mutant's death. That may sound like a crazy fan theory, but it's one which has actually been confirmed by director James Mangold!
In that 2013 movie, Yukio, who can see the future, tells Wolverine that, "I see you on your back, there’s blood everywhere. You’re holding your own heart in your hand." A scene like that plays out later in the movie but after one fan compared that prophecy to how the hero dies in Logan, it turns out that the director may have had Wolverine's demise on his mind four years before that was released!
In this instance, Wolverine's "heart" is his daughter X-23, and while this would normally feel like a stretch, you can't really argue with it based on the response from Mangold on social media today.