Out of Order: Some episodes that were intended for season 4 were pushed up to the third season. In turn, some season 3 episodes were pushed back - most ridiculously the episode "No Mutant Is An Island" which is supposed to take place during Jean's death between the Phoenix Saga and the Dark Phoenix Saga.
The Canadian Wolverine and the American young!Cyclops are both played by Australian actors. Americans Xavier and Juggernaut and the Polish Magneto are all played by British actors (although in the case of Juggernaut and Xavier, their nationalities are never mentioned and they don't hide their natural accents so one could assume that the movie versions were simply from England) — which also includes the Scottish James McAvoy and the Irish Michael Fassbender. The German Nightcrawler is played by the Scottish Alan Cumming. Storm, who is from Morocco, and the Canadian Sabretooth are both played by Americans (by two different Americans, in the case of Sabretooth). The Americans Rogue and Jean Grey are played by a Canadian and a Dutch actress respectively, while the American Iceman is played by a Canadian. The Russian Colossus is also played by a Canadian but like the Xavier and Juggernaut examples above, the movie version is never given a clear nationality. Phew.
In First Class, Magneto is German-Irish and Xavier is Scottish (and the nationality is still unclear, as he lives his childhood in New York but graduates in Oxford). Not to mention Nick Hoult (English), and Rose Byrne (Australian) playing Americans.
The CIA Agent who is the first to try and stop Shaw when he invades the CIA compound is Tony Curran, better known for playing Vincent van Gogh in Doctor Who, or being in the The League of Extraordinary Gentlemen movie, along with Jason "Azazel" Flemyng. Curran also played a knight in an episode of Primeval when Flemyng was in it, making this at least the third thing they're been in together.
The Other Darrin: Apart from younger versions (the most notorious being Xavier, Magneto and Mystique; the most infamous being Sabretooth from X-Men to Wolverine), Kitty Pryde has been three actresses (with Ellen Page being the first to reprise the role), and the Pyro in the first movie is not Aaron Stanford.
Bryan Singer brings along cinematographer Newton Thomas Sigel, writer Michael Dougherty (and in the second, editor-composer John Ottman, who was busy during the first)... and neglects them the third by dragging them along for Superman Returns. Everyone but Dougherty is in Days of Future Past as well.
In First Class, Matthew Vaughn brought his producer/writing partner Jane Goldman, and actor Jason Flemyng (who even though of not doing make-up heavy roles after Clash of the Titans, but opened an exception to Vaughn).
Refitted For Sequel: The bathroom set in X2 was originally built for a flashback scene Cyclops discovering his powers in the first, that was left before being shot.
Singer Glenn Danzig of Misfits was the first choice for Wolverine (back when Carolco Pictures held the film rights) since he fit the character's build. After the long development hell period, Danzig had aged and it was decided to seek other options.
On the DVD commentary for the second film one of the writers mention their ideas for adapting the Dark Phoenix Saga, with Jean committing suicide by telekinetically forcing Scott to look at her and then removing his visor.