That's always been something that bugged me. I really liked The Wolverine, I felt it did its job (make a movie about Wolverine stabbing shit) pretty much perfectly. It had a nice self-contained plot and cast, and it didn't overburden itself with references to other X-Men elements like Origins did.
But...after Days of Future Past, did any of it happen? Because Cyclops, Jean and Xavier are both still alive after DoFP, which means X-Men 3 didn't happen, which means Wolverine is still with the X-Men and not in a cave somewhere talking to bears. And obviously, he's got his adamantium claws back as of Logan, which means either a) The Wolverine didn't happen, b) it did happen, but he never got his claws cut off by the Silver Samurai, or c) that Magneto decided to be a good guy again and used some of the Silver Samurai's leftover adamantium to give Wolverine his claws back.
I'd be real upset if it was A, and even B is kind of a cop-out, and I don't see how C would ever happen unless Magneto did a full heel-face turn after X-Men 2. Maybe it'll be explained in the film. "Thank God we invented the, you know, whatever machine."