Plot hole: When Jubilee and Iceman are tied up, Jubilee has metal "mittens" over her hands that prevent her from using her powers to escape, but Iceman notes that they failed to learn about his powers and uses his ice powers to break free from his ropes. Iceman was in his ice form when X-Factor attacked him and Jubilee, and they also know that he previously attacked their compound, so they should have known that he had those abilities. (00:13:40)
Plot hole: This episode showed that Beast was an original member of the X-Men and also depicted the original X-Men battling Magneto. However, when Magneto attempted to break Beast out of jail in the season 1 episode "Enter Magneto", Beast said to him "I don't believe we've met. Magneto I presume."
Plot hole: Nightcrawler spends a good amount of time trying to escape the angry mob on foot when he could simply teleport away from them. (00:02:00 - 00:02:40)
Plot hole: Some of the footage Magneto is showing the delegates at the U.N. meeting includes footage Magneto could not possibly have had access to even if such footage existed, such as the X-Men having mission briefings in the War Room, the Morlocks living in the sewers or Warren Worthington emerging from being buried under several feet of snow at his secluded home in the mountains. (00:03:10 - 00:04:05)
Plot hole: This episode establishes that Magneto lost his family in the Holocaust, which is taken from the comics. However, the season 1 episode Enter Magneto established that Magneto lost his family when a guerilla army occupied his country.
Beyond Good and Evil: Part 1 - S4-E8
Plot hole: Gambit remarks that Shard is his kind of time traveler. However, Shard was inside the mansion and Gambit was outside when he said that, and he had never previously met her, so there was no way he could have known who she was without having even seen her or even that she was a time traveler. (00:17:20)
Beyond Good and Evil: Part 1 - S4-E8
Plot hole: Beast comments on Mr. Sinister's new-found time travel abilities. However, Beast has no way of knowing that Mr. Sinister is time traveling. He only knows that Mr. Sinister is using portals, which could just as well be for teleportation. (00:18:40)
Secrets, Not Long Buried - S4-E15
Plot hole: At the speed Cyclops is traveling in his mini-jet when he passes Watchdog's tower, he would have been long out of range before Watchdog could force him out of the air into a crash landing, considering that Watchdog had to take time to alert Solarr of Cyclops' presence and be ordered to knock him out of the air. (00:02:30)
No Mutant Is an Island - S5-E4
Plot hole: When Killgrave's bodyguard dumps Cyclops face down in the pool and leaves him for dead, it is night time. When Sarah is shown to have successfully resuscitated Cyclops, it is broad daylight. If Cyclops had been floating face down in the pool for several hours then he would surely be dead. No amount of CPR would have brought him back. (00:15:45)
Answer: It appears a number of factors led to its demise. It was originally intended to air for 65 episodes, but its popularity extended that. However, there were continual production quality problems, issues regarding whether the content was suitable enough for children, as well as financial considerations that finally led to it being ended.
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