Factual error: In the Shinkansen fighting scene, the railway line is seen having color light signals along its way. But the Shinkansen uses a signalling system that doesn't involve the use of light signals at all.
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: 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)
Visible crew/equipment: In the funeral scene where Logan is attacked, he gets shot and knocked down. The camera pans towards Logan and we get a close up of his exposed claws. If you look in his fist you can see Hugh Jackman is holding on to a round gold colored object in plain view. This is the handle Hugh Jackman holds on to for his fake movie prop claws.
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.