Now that we've had time to absorb just how badly "Wolverine" sucks (99% of people who actually care if it was good or not went before Sunday) and the more-important "is the movie any good?" objective review is out of the way... now for the nitpicky movie-geek stuff regarding all the things that just don't make sense.
This of course comes with a hellaciously big SPOILER WARNING!!!
-Allowing for the sake of argument that pre-surgery Wolverine's bone-claws can be chalked up to an outgrowth of his accelerated healing powers (i.e. if his body can regenerate cells and tissue so quickly, it can also rapidly-generate bone growths) where exactly do they "go" when he's done with them? Do they fall off? He can't just absorb them back in - the matter would have to go somewhere.
-Speaking of claws, why would coating his main skeleton with metal cause his claws to take the shape of perfectly set, filed and weighted knife-blades?
-For THAT matter, if his claws are biological WHY do we see the blades set into his forearms on a spring-and-hinge system in his x-rays in "X-Men?"
-Given that the story basically "reveals" that the infamous Three Mile Island disaster was actually a cover-up for the damage caused during a brawl between Wolverine, Sabertooth and Weapon XI, that places the events of this story in and around about 1979. Given that, where did Stryker get all his brand-new looking computer tech? (His team's guns and other gear also look pretty post-90s, overall.)
-The opening scene's subtitle informs us that young-Wolverine's family's estate is in "Northwest Territories Canada" in (IIRC) 1864. The country we call Canada did not exist by that name until 1867, and the Northwest Territories weren't PART of it until 1870.
-No one in this film calls Victor Creed "Sabertooth," but that was the "real name" of the Sabertooth encountered in "X-Men," so it stands to reason that this is the same guy. He never brings up that Wolverine is his brother in that film, though you'd imagine he'd be surprised to see him after all this time. Now, maybe he ALSO got shot with a magic amnesia-bullet at some point, fine... but don't you think this connection might've come up when he and Toad were having their minds looked-around-in/controlled by powerful psychics (or am I misrecalling that part?)
-Evidently, Silverfox's powers of psychic suggestion are so strong that her "orders" are still in effect at a range of what would have to be hundreds of miles AND after her death. If so, why is Stryker spending so much time making a remote-control ninja frakenmutant when he has someone already in his employ who can turn ANYONE into an unquestioning soldier/assassin/whatever by tapping them on the shoulder?
-If Emma (Frost?) Silverfox's skin turns into literal diamonds - the hardest substance on earth - couldn't she have slipped her cage any time by simply dragging her hand back-and-forth across the bars really fast? It's not like any WEAPON they have can harm her.
-Professor X contacts young Cyclops while he's IN Three-Mile Island and picks him up there, which means that both of them know that the "meltdown" was actually a mutant fight. Wolverine, though he's lost his memory, is ON said Island when he wakes up and must at least know he was "on hand" shortly-after and likely during whatever went down there. Apparently, the "coincidence" of this has never once come up between these three men when they meet again years later; and somehow I doubt "the first thing I remember is waking up in the remains of 3 Mile Island" would NOT be mentioned during his various psych-sessions at X Mansion.
-Agent Zero has the mutant power to rip-off scenes from "Equilibrium," which makes him a master gunfighter. He employs these skills when sent to hunt a freshly-escaped Wolverine. During said hunt, we eventually know that Stryker already has super-special bullets that can both pierce Wolverine's skeleton AND give him amnesia. Agent Zero is NOT using these bullets because...?
-How did they actually convinced him that Silverfox was dead, since his feral senses of hearing and smell would tell him IMMEDIATELY that her heart was not stopped and that it wasn't her blood.
-Weapon XI/Deadpool's optic-blast can cut through solid stone AFTER he has been beheaded, but it doesn't go all the way through Victor Creed?
- Young Cyclops is blindfolded the whole time and never actually sees Wolverine, fine. But all the OTHER kids who go off with Xavier alongside him DID. You'd think at some point he'd ask about how the cages got opened, and that one of the dozen or so others would mention "gut with knife-hands did it," yet this never comes up when he meets Wolverine again as an adult?
...did I miss any?