Sidney Iwanter, an executive at Fox Broadcasting Company, originally planned on "ending" the series with a big bang ("Beyond Good and Evil - parts 1-4"). They even had planned to have characters leaving the team at the conclusion, but at the last minute Fox asked for more episodes. Unfortunately, at the time Marvel Entertainment Group was filing for bankruptcy and could not afford to produce more episodes, so Saban Entertainment funded them directly. This explains why the last six episodes looked different than the previous 70. So the show officially "ended" things again with Graduation Day (1997).
David Hemblen (the voice of Magneto in the show) was offered the chance to play Magneto in the X-Men live action movie. Hemblen wanted the role but he was forced to turn down the role due to scheduling conflicts with his show Mission Erde: Sie sind unter uns (1997).
The sound effect used for Magneto's magnetic powers is the same sound effect used for the Klingon cloaking device in Star Trek III - Auf der Suche nach Mr. Spock (1984).
As of July 2022, the series is put in story order on Disney+, meaning episodes that aired later that were meant to be after specific storylines are now where the creators meant for them to be.
This X-Men series is one of the first animated shows to be serialized, with each of the episodes continuing into the next, although most of them also stand alone as separate shows. After "The Phoenix Saga" aired, the remaining episodes that aired were not in the correct continuity order. Because the bulk of episodes were being animated with many different studios, the writers decided not to continue with linear storylines like the first two seasons, as many would likely air as soon as they became available. Continuity problems became so bad that No Mutant Is an Island (1996) and episode Longshot (1996) did not air for two years after they should have, thanks to animation quality issues. "No Mutant is an Island" was *supposed* to explain Jean Grey's return, setting up the Dark Phoenix Saga.