Continuity mistake: Logan boards a Gulfstream G450 on his way to Tokyo. The interior shown next is very similar to a G450. The next external shot of the aircraft shows a Dassault Falcon 7X. Apparently he jumped onto a new aircraft mid flight. (00:17:00)
Suggested correction: Actually the plane in the air is an earlier version of the 12 window Falcon 900. The missing wing tip fences date it to late '80s through the '90s before the EX, DX and LX series updates.
Continuity mistake: When Viper confronts Shingen, she removes her left glove twice.
Continuity mistake: In the fight with the silver samurai, after Wolverine loses his claws from one hand, he takes a sword. Twice he goes to the ground, and in that shot there is no sword in his hand, then it appears again.
Continuity mistake: As Wolverine bids farewell to Mariko in the next to final scene on the airport tarmac, Yukio is visible in the background of the shot standing at the foot of the stairs, where she receives a green box which she tucks under her arm. The scene cuts to Mariko, when it moves back to Wolverine, Yukio remains in the background but the green box has disappeared.
Continuity mistake: When Mariko and Logan are eating, Logan uses a fork and leaves his chopsticks sticking straight up out of the bowl. Mariko removes them and lies them flat, saying it's bad luck. Then they keep talking and suddenly the chopsticks are vertical again without him touching them.
Continuity mistake: When Logan fights with Shingen, Yukio gets a small wound on the left side of her face which increases in size after the fight.
Continuity mistake: After Logan takes out the spider from his heart he has blood on his abs, which disappears when he fights with Shingen.
Continuity mistake: When the red headed Asian girl pulls the car over in the beginning, Logan is looking at her. But the camera changes angles to his perspective and he is suddenly looking straight forward.
Continuity mistake: When Yukio is holding a knife to Logan at the grandfather's place, it alternates from being vertical to slanted between shots.
Continuity mistake: In the bar Logan drops just a bit of liquor on the guy with the arrow on his hand, but in the next shot a lot more is flowing over the wound.
Continuity mistake: Just as Logan and Mariko are about to enter the room at the "love hotel", the door opposite their room shows a teddy bear on the door, but when it switches to the view from inside their room the opposite door now shows a stethoscope.
Suggested correction: They're two different doors and the teddy bear room isn't opposite their room. The teddy bear room is #30 and the stethoscope room is #31.
Continuity mistake: A ton of arrows pierce Logan back but later they show his shirt and there are no holes in it.
Continuity mistake: The note that says "come and get her" in blood changes when Yukio pins it to the wall. The letters are written differently.
Suggested correction: The letters are in the same way.
Watch the scene again. They are different, they are in a different position too.
