Other mistake: Intro Mission 2: When the flying torsos of the security bots go to the pods to connect with arms and legs, they go in and turn around as their limbs begin connecting. The metal tentacles on them just instantly vanish in a jerky animation.
Continuity mistake: Intro Mission 1: During the opening cut scene, Ben is about to go out an air lock to go close the Adamantium shields on the space station. When the level starts, Ben is in the same air lock, only now it is much larger.
Continuity mistake: Intro Mission 1: At the end of the level, you go to the edge of part of the space station that was just destroyed, and you hear Reed yell to Ben he has to jump. You go to the edge and instantly a cut scene starts. When it does, there is now a weird looking sensor array or something on the deck right behind him, that was not there as you moved him to that spot.
Continuity mistake: Intro Mission 1: During the opening cinematic, Ben is in his space suit and daydreaming about how they got there. When Reed speaks to him to snap him out of it, he is facing out of the air lock. You can see a reflection of the space station parts on his visor. But when the camera angle cuts to his back, what is in front of him is nothing like what is reflected on his visor.
Other mistake: Intro Mission 1: In the opening cinema cut scene as Doom tells Ben that their futures are all depending on him, Reed is in the background typing on a computer. He begins putting his right arm down towards his side with a bent elbow. Half way down his arm suddenly jumps to being almost all the way down in a jerky, glitchy animation.
Bug: Intro Mission 1: If you take Ben off the space station, Reed starts shouting at him to stay on course. If you go off too far, it is game over. Hit the restart option and then press A to skip the cinema cut to return to the level. As soon as the level begins and you hear Ben begin to breathe, hit the pause button. This leads you into the pause menu, and this is where the glitch happens. You will hear Ben inhale sharply during the menu, despite you not being able to hear him when paused, and he sounds almost like Darth Vader. But before his breath is finished, you hear part of Reed's rant play, where he is just yelling the word "Course!" This plays rapidly on a loop of hearing Ben breathe once, followed by Reed yelling "Course" over and over again until you unpause it. The glitch ends after that.
Other mistake: Intro Mission 1: Once the characters get their powers, pressing Z uses up their "Cosmic." Cosmic is the blue bar underneath the green health bar. On Mission 1 of the Intro level, it is before the cosmic cloud hits the station, thus none of them have any powers or cosmic yet. However, you are controlling Ben in a space suit out on the space station, and he has a blue bar of cosmic below his health. If you hold down Z, you see the Cosmic begin dropping from 100 and the blue bar move.
Other mistake: Brooklyn Missions 1&2: When a fire escape is broken and collapses to the ground, it kills any enemies on or under it, and hurts any of the Fantastic 4 in its path unless they, like Ben, bring it down. Yet any civilian walking by, even being right under it when it falls, is completely unscathed.
Plot hole: Brooklyn Mission 2: After Reed and Sue confront Ben, he smashes down a fence and takes off. Only on the other side of the fence are 3 members of the Yancy Street Gang. The fence even hits these three guys and Ben runs between them. Yet, despite the fact in the previous mission, Ben took out many of their fellow gang members, including their leader, they act like they don't even see Ben. They ignore him completely as he hits them with the fence and plows between then. And then they charge at Reed and Sue to attack, and they have never even seen Reed or Sue before, nor has any of their gang.