After battling the Marauders, Angel lost his wings, Nightcrawler was placed in a coma, Colossus became paralyzed and briefly stuck in his armored form, and Shadowcat was gradually "phasing" herself out of existence. (Uncanny X-Men #212)
The Morlocks, outcast mutants inhabiting New York City's sewers, were practically wiped out by Mr. Sinister's Marauders. Sinister believed the Morlocks to be scientifically useless in his quest for global mutant domination. (Uncanny X-Men #210-#213)
Cyclops' first wife, Madelyne Pryor, was a clone of then-believed-dead Jean Grey. She was created by Mr. Sinister to meet Cyclops and ultimately sire a mutant child that sinister believed would have powers vast enough to assist him in Apocalypse's destruction. (Uncanny X-Men #241)
In an alternate future called "Days of Future Past," the Sentinels had conquered the United States! They'd killed most of the X-Men, Avengers, Fantastic Four and others, and threatened to conquer the world. (Uncanny X-Men #141-#142)
Rogue's super-strength, invulnerability and flight powers don't really belong to her. When Rogue was a bad guy, she maintained contact with Ms. Marvel too long, and Rogue's mutant power permanently stole Marvel's powers. (Avengers Annual #10)
When Wolverine pops his claws from their sheath inside his arm, the claws actually pierce the skin on the top of his hands. His healing factor heals the laceration almost instantly.
Cameron Hodge was hired as X-Factor's original P.R.guy. He turned out to be a mutant-hater who led the terrorist group the Right, and eventually set up shop in the mutant-discriminatory country of Genosha. (X-Factor #1, X-Factor #17)
The first X-Factor roster was the five original X-Men who took advantage of public anti-mutant sentiment by posing as mutant hunters (they actually located and protected mutants). In their costumed identities they called themselves the X-Terminators. (X-Factor #1)
Not only is Professor Xavier's School for Gifted Youngster's a cover for Xavier to teach his pupils how to use their mutant powers, but it's also a real school that gives a high school and college education. (Uncanny X-Men #7)
Beast wasn't always a blue furry guy. He started out as a human with abnormally large hands and feet, and later ingested an experimental serum that accelerated his mutation, causing grey fur to grow all over his body, his canines to grow and his already superhuman abilities to increase. His grey fur soon turned blue. (Amazing Adventures #11)
The first time Professor X met Storm, she was a young thief in Cairo who picked his pocket. He would return years later to recruit her to his new X-Men Team. (Uncanny X-Men #117)
For all her genetic schooling, Moira MacTaggert couldn't help her son Proteus. A mutant who can alter reality, Proteus needed human hosts to survive. On a rampage, he'd killed several people, including his father. But Proteus ultimately succumbed to his one weakness: metal, in the form of Colossus' mighty fists. (Uncanny X-Men #125-#128)
Jean Grey was not the original Phoenix. When crash-landing from space, a cosmic entity took her place and left her in a cocoon at the bottom of New York's Jamaica Bay. She lay there for years until the Avengers discovered the cocoon, and the Fantastic Four revived her. (Uncanny X-Men #101, Avengers #263, Fantastic Four #286)
Charles Xavier entered college at age 16, and earned a bachelor's degree in biology from New York's Bard College (he graduated in two years time), a master's in both genetics and biophysics from England's Oxford University, a Ph.D. in anthropology from New York's Columbia University, a Ph.D. in psychiatry from Oxford and an M.D. from Oxford. (Official Handbook of the Marvel Universe #8)
Erik the Red is never what he seems. The first "Erik" was Cyclops wearing a disguise to foil Mesmero, Magneto and their Demi-men; the second was a Shi'ar agent named Shakari who was ordered to kill Lilandra; and the third was Magneto wearing a disguise to expose Gambit's past crimes. (Uncanny X-Men #49-#52, #105, #350)
When Cyclops wished to lead the X-Men after a long absence, then-leader Storm offered to duel him for the position. The powerless Storm Beat him, and Cyclops left the team altogether. (Uncanny X-Men #201)
Thunderbird was the first full-fledged X-Man to die in the line of duty, trying to stop Count Nefaria from escaping. (Changeling, who died years earlier posing as Professor X, was named an Honorary X-Man after the fact.) (Uncanny X-Men #95)
Magneto is Quicksilver and Scarlet Witch's father. Though the three of them were all part of the original Brotherhood of Evil Mutants, none of them would find out the truth until much later. (Vision and Scarlet Witch (first mini-series) #4)
While trying to save Captain Britain from a time anomaly, Rachel Summers was hurled into the far future and became Mother Askani, the leader of a rebellion against Apocalypse. There she brought young Cable to the future, where he'd be trained to fight. (Excalibur #75, The Adventures of Cyclops and Phoenix #1)
Wolverine agreed to take care of a young Japanese girl named Amiko at the request of her dying mother. The girl is presently being watched over by Logan'y ally, Yukio. (Uncanny X-Men #181)
When Xavier left Earth with the Shi'ar to heal injuries inflected on him by an anti-mutant mob, he asked Magneto to run the school for him. Magneto did so under the name, Michael Xavier, but eventually left, unable to convince the New Mutants to follow his points-of-view. (Uncanny X-Men #200, New Mutants #75)
Before she joined the X-Men, Rogue was a member of Mystiques New Brotherhood of Evil Mutants. She came to Professor X seeking his aid with controlling her powers. (Avengers Annual #10, Uncanny X-Men #158, #171)
After their battle with the Adversary, the X-Men were saved by the celestial being called Roma, who gave the X-Men the ability to not be detected by any mechanical or magical devices. Since then, the ability has faded away. (Uncanny X-Men #227)
Cannonball once apparently died and returned to life, and was therefore assumed to be an "External," a rare mutant who is able to live forever. (X-Force #7)
Some X-Men aren't mutants. Mimic gained his power to duplicate others' powers after accidentally breathing in a strange gas in his father's lab, and Longshot is a genetically engineered humanoid from another dimension. (Uncanny X-Men #19, Longshot #1-#6)
Xavier once had a shapeshifter named Changeling pretend to be him while the Professor secretly prepared for an alien invasion by the Z'Nox. When the "fake" Xavier died in battle, the X-Men even held a funeral. The genuine article returned a short time later. (Uncanny X-Men #42)
Cyclops can't turn off his optic blasts. When he was young, Cyclops was thrown from a burning plane and suffered a head injury upon landing, damaging the part of his brain that would've controlled his mutant powers. (The Marvel Saga #4)
Brother's Cyclops and Havok's mutant powers are both capable of incredible destruction, but for unknown reasons, their powers can't affect each other. (X-Factor #61)
Psylocke was once Caucasian (British, actually). Her mind was transferred into the body of an Asian assassin named Revanche, whose mind was transferred into Psylocke's. Dying from the Legacy Virus, Revanche had herself killed by Matsu'o Tsurayaba. (Uncanny X-Men # 257, X-Men #22, #31)
Phoenix was not supposed to die at the conclusion of Uncanny X-Men #137. The creators originally intended only for Jean Grey to be stripped of her powers, but the powers that be felt that she deserved a harsher fate. (Phoenix: The Untold Story)
Nightcrawler was the first of the New X-Men team recruited by Professor X. He was about to be killed by a mob in his native Germany before the Prof stepped in. (Giant-Size X-Men #1)
Charles Xavier isn't in his original body. It was destroyed when a Brood Queen "hatched" from it, and alien technology put his brain into a cloned body that could walk. His new legs would later be crushed in a fight with the shadow king. (Uncanny X-Men #167, #280)