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)