Continuity mistake: For the first half of this episode, Magneto is wearing a red dress-shirt with a black tie under a dark gray trenchcoat. After he is captured by the High Evolutionary, he is suddenly wearing his usual red and purple costume. Even if Magneto brought a change of clothes with him, it's extremely unlikely that the High Evolutionary would change his clothes for him.
00:03:40 - 00:12:40Phaneron
Continuity mistake: The style of the lettering on Magda's gravestone changes after the goat-woman runs away from Magneto. There is also a stone that was next to the grave when it is first shown that has suddenly disappeared in the same shot of the goat-woman running away.
00:09:10 - 00:09:45Phaneron
Continuity mistake: When Bova is bringing the baby twins to Django and Marya's house, the arm she is carrying the respective twin in changes depending on the shot. When she is first shown walking towards the house, she is holding Wanda in her left arm and Pietro in her right. When she is walking up the steps to the door, she is carrying Pietro in her left arm and Wanda in her right. When the shot changes after Django opens the door, the twins have switched arms again, and then again when she hands the babies to Django and Marya.
Continuity mistake: When Xavier is surrounded by a group of mutants in his subconscious, if you look at Quicksilver you can see that the colorist made his shirt flesh-colored. You can tell he is supposed to be wearing a shirt because the lightning bolt design is still going across his torso.
Continuity mistake: During the battle at the end, Cyclops uses the crystal statue he brought with him in the fight by throwing it into the air and uses it to refocus his optic blasts on a crowd of attackers. After the battle is over he gives the statue to Dr. Prescott without ever having retrieved it.
00:18:55 - 00:20:20Phaneron
Other mistake: When the group of mutants are listening to Solarr's speech, in one continuous shot of ten of them that lasts at least four seconds, they are all standing completely still, not one of them moving a muscle, blinking or making the slightest adjustment in their facial expressions.
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.
Other mistake: After Rogue absorbs Wolverine's healing powers and purges the transformation spores from her system, she reverts back into human form including losing the tail that she grew. Given that the tail protruded from her backside, there should have been a hole in the back of her pants afterwards, yet there is none.