As far as I know, X-Men 1, 2, 3 and the start of Days of Future Past form an original timeline. Then in Days of Future Past, Logan goes back in time and creates a new timeline. Later in this new timeline, Apocalypse awakens in 1983 and wreaks havoc.
This raises a huge question. Where is Apocalypse in the original timeline?
They have no mention of him nor any strange events in 1983 and everyone acts like mutants are new to them. Alternatively, if he was sleeping under Cairo throughout the entire original timeline, how did Logan's actions cause him to awaken in the new timeline but not the original one?