Plot hole: Magneto states that he went to Washington, DC to witness Senator Kelly's assassination. But Magneto had no way of knowing about the assassination plot. Mystique was the one who was attempting to assassinate Kelly, and Apocalypse was the one who carried out the order. At this point in the show, Magneto had not worked with either Mystique or Apocalypse, and it's highly doubtful that Mystique would leak the plot, since it was supposed to be covert.
Continuity mistake: The exploding playing card that Gambit uses to destroy a few Sentinels and draw the rest above ground is cleverly shown to be the ace of spades (also known as the death card in some folklore), but the card he is shown charging up before the Sentinels see it is the 2 of diamonds. (00:12:10)
Continuity mistake: When Gyrich is in the car trying to get Trask on the phone, he is shown to be sitting in the backseat on the passenger side (note the windows immediately to his right and behind him). When his driver crashes the car into a tree, Gyrich is shown exiting the car from the front passenger seat. (00:08:00)
Continuity mistake: When Trask turns the laser onto the propane gas tank, it is on Master Mold's left. When Master Mold reaches down to try and stop the laser before it causes the tank to explode, it is now on his right. (00:16:04)
Continuity mistake: When Rogue is calling out to Gambit just before Jean and Senator Kelly exit the mine shaft, the X logo on her chest is a yellow X on a red background, when it should be a black X on a red background. (00:17:57)
Continuity mistake: When Jean is using her telekinetic powers to rescue Senator Kelly from Master Mold's lab, she drops him on the floor in the middle of the lab. When Cyclops gets blasted by Master Mold after he and Jean run to grab Kelly, Jean and Kelly are suddenly inside the mine shaft. A couple of shots later, Jean and Kelly are now standing at Master Mold's feet. (00:15:42)
Continuity mistake: When Gambit is asking Xavier why the X-Men must all die to save Senator Kelly, the top of Wolverine's mask is incorrectly colored blue. A few shots later, this portion of the mask is correctly colored yellow, but then the portion of his mask by his right cheek is also yellow, when it should be black. (00:09:48)
Continuity mistake: When Master Mold is telling Trask that mutants are humans, Trask's right hand is raised near his face. When the shot changes, his hand is suddenly lowered at about waist-level. (00:15:11)
Revealing mistake: When Jubilee is saying "What's anybody waiting for," her arm passes through Wolverine's body. (00:10:40)
Continuity mistake: When Trask's voice is first heard coming from Gyrich's cell phone, the phone is in the top left corner of the floor tile. When the shot changes, the phone is now in the center of four smaller tiles. (00:09:12)
Continuity mistake: When Gyrich's gun slides over next to Cyclops' feet after Wolverine tackles him, you can see Cyclops, Rogue, and Storm are standing at the entrance of the Lincoln Memorial. When the shot changes, the three are no longer near the entrance. (00:09:07)
Continuity mistake: When Beast is first shown in his prison cell, the X logo on his waistband is black with a red background. When Jubilee hugs him, it is now a red x on a yellow background. (00:19:51)
Factual error: When Senator Kelly is giving his campaign speech, the U.S. flag behind him is missing one stripe and has at least two too many stars. (00:19:30)
Continuity mistake: At the beginning of Senator Kelly's campaign speech, his campaign button is predominantly white with some blue at the top and bottom. When the shot changes, the majority of the button is now blue, with only a small portion in the center being white. (00:19:20)
Factual error: When a parachuting Xavier is about to land, you can see his legs are bent at the knee to brace for landing. Since Xavier is a paraplegic, he shouldn't be able to do this. (00:19:14)
Revealing mistake: When Xavier is parachuting towards the ground, the stars in the sky are flickering on and off. (00:19:00)
Continuity mistake: When Jubilee is saying how much being a member of the X-Men means to her, one shot shows Gambit looking despondent, and the lines on his collar armor are missing. (00:10:53)
Continuity mistake: When Wolverine is telling Jubilee that she isn't going on the mission, the parts of his mask next to his cheeks are yellow, when they should be black. (00:10:41)
Continuity mistake: When the X-Men are flying to where Magneto is, the sclera of Gambit's eyes are colored white, when they should be black. (00:04:37)
Continuity mistake: When Cyclops is running through the mine to search for Wolverine and Gambit, he uses his visor to track their location. When the shot changes to a first person view through Cyclops' visor, the background is merely moving up and down. If he was running as the previous shot had shown, the objects in the background from his point of view would become larger as he got closer to them. (00:16:50)
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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