As franchises go, the X-Men movie series is pretty badly riddled with plotholes thanks to the film-makers' fondness for confusing timeline shifts and alternate universes that seem to contradict the usual rules of continuity. But then, they never really seemed to care, so it's not at all surprising.
Of all of those plot-holes, the most infuriating came at the end of X-Men: Days Of Future Past, when Wolverine was fished out of the bay by Stryker and his team and discovered to be alive. It initially appeared that this was how Logan would end up in the Weapon X project and have his mind wiped and adamantium added to his skeleton.
But then it turned out that Stryker was in fact Mystique, so Wolverine was presumably safe from the real Stryker and wouldn't end up being Weapon X. Except, he did, as we saw in X-Men: Apocalypse's Weapon X breakout sequence.
That scene seemed to completely forget the fact that the Stryker who rescued Wolverine was Mystique and accepted that the timeline had simply continued on as if it was the real Stryker. So Logan still ended up being tortured and reprogrammed, suggesting that somewhere along the line, Mystique just let him go (despite hinting at plans for him in that rescue scene) and the real Stryker managed to convince him to take part in the Weapon X programme (or captured him). In short, it was a dropped ball.
Bryan Singer seemingly knows that fans had concerns over the scene at least, as a new post on Instagram has revealed that the Mystique twist was added late in the day:
While the honesty that the twist was added late is refreshing, it still makes no sense. Sure, it establishes that Mystique was going to be a mutant helper, but there's no hint of that in Days Of Future Past, so it comes off as something of an ass-pull. And it doesn't line up with the fact that he still ended up becoming a Weapon X test subject.
And it doesn't look like we're ever going to get an answer to what happened in those intervening years.