In the first showing of the episode where the X-men fight Apocolypse in Muir Island, the episode ends with a shot of the X-mansion in good condition, but the second and third showings have a different ending where the X-men discover that the X-Mansion was destroyed (Juggernaut destroyed the Mansion).
When the episode "A Rogue's Tale" first aired, it was called "I Remember Mama." It became known as "A Rogue's Tale" starting with the first repeat.
Mr. Sinister's original voiceover at the end of the initial airings of "Final Decision" was replaced when the character was cast for season 2.
In "A Rouge's Tale" (AKA I Remember Mama), during the original airing, animation cells for Jean Grey inexplicably vanish from for a number of frames during Rouge's crazed flight around the Mansion.
When Wolverine is attempting to break free from the ice in the episode "The Phoenix Saga pt.3: Cry Of The Banshee", for a single frame you can see a production note indicating to cut the print. This frame was removed and replaced in later airings.
The first season of X-Men, when aired on FoxKids, featured CGI character profile models during the end credits. Later airings replaced these credits with those similar to season 2. When the fourth year episodes began, short clips from past episodes were filtered into the credits for the original airings. When the final year's worth of episodes aired, the series recieved slightly altered intro animation and music. When reruns of the series moved over to UPN for a short while, all of the aired episode intros and credits were replaced with brand animation, featuring Cable among the regular X-Men.
After Iona Morris quit voicing Storm, some early episodes were re-dubbed by Alison Sealy-Smith however poorly and sometimes unsynchronized (most evident in "Enter Magneto") There were often alterations in scenery and dialogue made to first season episodes after the initial airings, such as the original ending of "Night of the Sentinels Part 1." The original ending had soldiers dressed in red and white armor hiding behind the door to the room the X-Men were about to enter, however reairings had the soldiers in green military fatigues.