X-Men essentially ushered in the modern age of comic book movies in 2000, but there was a big learning curve that Fox has had to adjust to. Timelines are pretty important, but because of some shaky continuity within the framework of the X-Men franchise, the timeline is a bit dicey. As such, it has been really difficult to explain how Deadpool and the upcoming Deadpool 2 fit into the overall X-Men timeline. A new fan theory has popped up online that could explain away this mystery and, as far as fan theories go, this is pretty believable.
Reddit user DToccs posted his theory about the Deadpool timeline to the Fan Theories subreddit. Basically, the idea is that Deadpool the movie, as we see it, is actually taking place in the world of the X-Men comic books that were established in Logan, which heavy fictionalize the events and characters of the movie universe we know. That's a little trippy to think about, but it makes a good bit of sense, all things considered. Here's how DToccs explains it.
"The X-Men comics in Logan are based on real people and real events, although they have been twisted and changed to the point where people like Xavier and Logan who lived the events can't even recognize them in the comics. The X-Men of the comics have some major changes from the real ones, all of the them (including Wolverine) wear colourful uniforms, Rogue can fly, Colossus is huge and Gambit a mutant from the 80s is contemporary with them...So I conclude that the Deadpool movies and the world they inhabit is actually the semi-fictionalized world of the X-Men comics that exist within the real world of the X-Men/Wolverine movies. Deadpool is a comic character loosely based on a real world mercenary from the 80s."
That would explain an awful lot about Deadpool and how it can possibly exist in the already established X-Men timeline. Even Wolverine in Logan explains the comic books saying, "It's a fantasy, kid. See that? Those are the names of the people who just made this [comic book]... They made this whole thing up. Okay? This whole... It happened once and they just turned it into a big f****** lie!" That sets up this theory nicely. DToccs also explained a bit more about why this theory about Deadpool may actually work and a lot of it has to do with Negasonic Teenage Warhead.
"In Deadpool, Colossus is distinctly different from the Colossus of the actual X-Men movies in every way, but he does resemble his character shown in the comics. Wade Wilson a mercenary who was active during the 80s and connected to the Weapon X program is instead placed in the 2010s as a contemporary of the X-Men, much the same way that the Gambit character in the comics is moved in time from his real world counterpart. The big thing though is Nega Sonic Teenage Warhead and what she represents. In Deapool the school is clearly active and is presented in such a way that you are to assume there are other young mutants there alongside her. However in the world of the X-Men movies, no new mutant has been born since the early 2000s when Zander Rice and Transigen deployed their targeted gene therapy. Negasonic Teenage Warhead is simply too young to exist."
Some good points are made, but it also seems like Fox is perfectly willing to just ignore clean continuity at this point in favor of making what they think is the best possible movie at that time. Considering how big of a hit Deadpool was, and how big of a hit Deadpool 2 is likely to be, they probably aren't overly concerned with explaining the continuity issues it may represent. That said, this is a pretty cool theory and one of the more plausible ones you're likely to hear.