Mystique sabotages Cerebro to put Xavier into a coma. Since X-Men: First Class is part of the same continuity, this means Mystique tried to kill a man whom she grew up with and loved as a brother and did not part with on hateful terms—and she did it all just to further an agenda.
Likewise the scene where Mystique impersonating Iceman convinces Rogue to leave the school because everyone hates her. Considering her defection in the prequel trilogy over feeling she won't be accepted, it's likely she knew exactly how Rogue was feeling and what buttons to press.
Now that we know from X-Men: First Class how Erik's mother died and how Charles became a paraplegic, Magneto's contempt towards guns here makes perfect sense.
In X-Men: First Class, it initially seems odd that Charles wouldn't encourage Raven to pursue a formal education (she sardonically responds to Amy's "What do you study?" with "Waitressing"), but when you recall what Mystique had said to Senator Kelly ("People like you were the reason I was afraid to go to school as a child"), then it becomes very clear that she and Charles were extremely fearful about the possibility that she might lose control of her power while in class.
Professor X's line "Experimentation on mutants—it's not unheard of" becomes more chilling when you take into account Bolivar Trask's examination and dissection of mutants in X-Men: Days of Future Past. Xavier would be thinking more specifically of Banshee's death and the torture Mystique endured before she managed to escape Trask Industries in the original timeline.
The Phoenix appearing in Alkali Lake is treated optimistically, with triumphant music to boot. However, the sequel reveals she is a complete psychopath who overrides Jean's original benevolent personality.
After X-Men: First Class had established that Charles and Raven grew up together as foster siblings, it's rather cruel of Mystique not to warn Professor X that Stryker was planning on attacking the school. Although she and Xavier are estranged beyond repair by this point, you'd think that Mystique would still be concerned about the safety of fellow mutants (especially those who are children) even if she had stopped caring about Charles like a brother.
Near the end, Stryker's grave warning is, "One day, someone will finish what I've started!", and mutant genocide actually does become reality in X-Men: Days of Future Past. The colonel wasn't making an empty threat at all; he was plainly aware of Trask Industries' progress on the Sentinels, and he knew it was only matter of time before the robots were sophisticated enough to slay even the most powerful mutants.
When Bobby informs Logan that there is no beer at the school, it's obviously because Professor X doesn't want to encourage underage drinking, but there is an additional reason for the alcohol-free environment: X-Men: Days of Future Past reveals that Xavier was a drunkard in between 1963 and 1973, so naturally his older, wiser self doesn't want to be tempted by drink and risk a relapse. Plus, if one of the students were to get drunk, a loss of control of their powers (or a misuse of them due to compromised judgment) could be more than slightly dangerous.
Lady Deathstrike dies when Wolverine injects her with a load of liquid adamantium, and she falls with an audible clank. Come 2014 in Death of Wolverine, Logan gets spilled on by a vat of liquid adamantium, covering him from head to toe.
Logan adds a whole new layer of this. "Someone will finish what I've started," Stryker says. In Logan, we find out that he probably meant Zander Rice, who actually succeeds in wiping out the mutant gene.
You know that cool scene in the beginning, when Xavier makes his entrance by freezing everyone? In Logan it's not so cool when one of the seizures Charles is now prone to sends out uncontrollable psychic waves that lock down everyone within his (very wide) range to the point of not even being able to breathe. We find out that the first time this happened, the X-Men and many and many other innocent people were wiped out, hence Logan beginning with Logan, Caliban, and an Xavier addled by a combination of his disease and the medications that prevent similar flare-ups being all that's left of the X-Men. Two throwaway moments in this film foreshadow how the entire X-Men saga ends as a "Shaggy Dog" Story, if not a Shoot the Shaggy Dog story, provided no one changes history DOFP style again.
After watching X-Men: First Class (which revealed that the young Xavier taught Lehnsherr how to achieve greater control over his power by finding the point between rage and serenity—the latter requires a happy memory), Magneto's line of "Charles always wanted to build bridges" as he's moving a large section of the Golden Gate Bridge seems to indicate that he's thinking about his old friend instead of his mother in order to attain serenity. And like his mother, Xavier—whom he loved as a brother—is now dead, so happy memories from their brief friendship in 1962 is all Magneto has left of him.
Erik truly seemed to grow fond of Raven in X-Men: First Class and spent decades with her at his side, then casually kicked her to the curb in this movie after she was hit with the mutant cure. The disheartened look in his eyes for being forced to do so, however, cannot be ignored either.
Six months after the film came out, Len Wein, who created Wolverine, died, joining his creation's cinematic counterpart.
Professor Xavier is shown suffering from an affliction affecting his cognitive functions with it being speculated to be Alzheimer's. Voice actor Jim Ward, whose credits include Xavier in Wolverine and the X-Men (2009), entered retirement in 2021 after he was diagnosed with Alzheimer's while seeking treatment for COVID.
The film features a cameo from the X-Men trying to hide from Wade, except two of them were missing. But nothing bad could've happened between Jean Grey and Mystique... right?
