Michael Bay reused stuff from The Island for Transformers: Dark of the Moon; Ridley Scott used material from The Shining for the end of Blade Runner; and Disney’s animated Robin Hood clearly has sequences that were traced over moments from both Snow White and The Aristocats.
So before you go judging the X-Men: Apocalypse filmmakers for their use of a clip from The Wolverine, consider that their sin is pretty minor compared to others (did you even notice it before we pointed it out?).
Bryan Singer and Simon Kinberg are surprisingly casual when they talk about the reused shot on the commentary, and while this is partially because they totally had the legal right to borrow footage from The Wolverine, the other reason is because this isn’t exactly a foreign activity in the movie world.