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)
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)
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)
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.