Other mistake: Wolverine shields Yashida from the blast, burning off all his hair. Somehow his pants manage to remain unaffected by this, as seen later when they are climbing from the pit.
Other mistake: When Logan loses his ability to heal, all his wounds stay, but his hands still heal after every usage of his claws - the skin on his hands is untouched.
Other mistake: When Wolverine has the parasite inside him he can't heal, but the holes for the claws heals just fine.
Answer: The chronology of the X-Men film series is, to put it mildly, somewhat screwed up. The first movie was released in 2000 and is described in an on-screen caption as being set in "The not too distant future", which isn't the most helpful statement, could be two years, could be ten years, who knows. The Wolverine is set about two years after the events of X-Men: The Last Stand, which is in turn about a year after the events of the first movie, so think about "the not too distant future", whatever that means, and add about three years onto that. This does mean that, yes, it is indeed set some decades after the events of the Origins movie, during which he lost his memories. It is, however, also set after a period during which he worked with Professor Xavier to regain some of his memories. It could therefore be suggested that Logan remembering his experience at Nagasaki represents that they had at least a partial success in recovering some of his memories.
Tailkinker ★