Dr. Jean Grey tells Professor X that Logan's healing ability "makes his age impossible to determine. He could very well be older than you, Professor." She doesn't realize how true this is because both X-Men Origins: Wolverine and X-Men: First Class have established that Wolverine is about a century older than Xavier! (James Howlett was born in the early 1830s while Charles' birth year is the early 1930s.)
At the end of the movie, Wolverine tells Rogue "I have some business to take care of up north." The RiffTrax notes that he's gone to help Santa Claus. In Rise of the Guardians, Hugh Jackman did end up helping Santa Claus, as the voice of the Easter Bunny.
Angela Bassett was offered the role of Storm, but turned it down. She later wound up playing the mother of Storm's ex-husband in Black Panther.
Kitty Pryde and Bobby's relationship being a Not What It Looks Like situation for him and Rogue in X-Men: The Last Stand takes on a slightly new light with Elliot Page's later self-identification as a lesbiannote In 2020, he later came out as transgender. Rogue really did have nothing to worry about.
For bonus hilarity, Iceman later came out himself in the comics.
Considering that Xavier can easily use Magneto as a marionette as long as the latter doesn't wear the telepathy-blocking helmet in X-Men: Days of Future Past, his words of encouragement in First Class ("When you can access all of that, you will possess a power no one can match. Not even me") now sounds rather hollow. It comes off as a little white lie that he made up on the spot in order to try to help Erik achieve the correct point between rage and serenity. In their natural state, Charles' ability is stronger than Erik's, no ifs, ands or buts about it.
Jennifer Lawrence plays a younger version of Rebecca Romijn. Lawrence later admitted to "stalking" Romijn's ex-husband John Stamos at a party.
The film adapted Death of Wolverine, including, as the title suggests, Wolverine dying. The one-shots kicking off Marvel Legacy sees the resurrection of comics Wolverine.
