Logan's in an alternate future & I figured out how. Remember when he "slipped back" in the 70's? My guess is that created an alternate branch where Wolverine's involvement ended. Charles went back home all depressed, Raven still blew away Trask, but Magneto sent the Sentinel program to shit anyway so everything proceeded about the same except humanity hated mutants more than ever. Without sentinels, they came up with another plan which led to Dr. Rice's virus. It also said in 2029 no mutants had been born for 25 years & the children at the end of Apocalypse in 2023 didn't look 19 years old. 8 of the heroes were also shown alive when in Logan it said 7 (probably including Charles & Logan) were killed by Xavier & I don't believe a single person there would've just abandoned Logan or Charles.