Plot hole: Nick Fury is talking with The Silver Surfer after Magneto has been defeated. Nick asks for ideas on how they can save the Earth, and the Silver Surfer states that they need his board. Nick asks what Doctor Doom wants with it, Silver Surfer says something about Loki and the power cosmic. With almost no chance of saving Earth, Nick decides to put in an outside call and has Agent Hill call Mr. Fantastic and the Invisible Woman. The scene switches over to the Baxter Building where Magneto crashes through the roof and Agent Hill then calls them and says to them "This is Agent Hill from S.H.I.E.L.D. Director Fury is in urgent need of your assistance. Agent Coulson is on his way to pick up Magneto." There is no way Agent Hill, Agent Coulson, or even anyone who works at S.H.I.E.L.D. could have possibly known Magneto was going to crash through the Baxter Building roof. Magneto had only crashed through the roof a few seconds prior to the call and they had no idea the precise direction in which Magneto was falling in. Agent Hill established through the call that Coulson was already on his way over to the Baxter Building, so even if Agent Hill had seen Magneto on the floor through the call, there is still no way she could have gotten the word to Agent Coulson that Magneto was there anyway.
Bug: Sand Central Station: In the first area of the level, Iron Man and the Hulk have to walk up to the Central Station whilst taking out the sand people up until they reach a huge truck between them and the museum. There will be two huge green levers for the Hulk to pull on. If the level is on Free Play and a standard sized character is standing between the huge green levers and you instantly switch to the Hulk standing in that same position, the Hulk will become stuck and won't be able to run or move away. He will be only able to rotate around in circles.
Audio problem: Rapturous Rise: Right before Magneto unleashes Rhino, he says "I see you've enjoyed playing with my pets. Let's see if you enjoy playing with this one." He is shown moving his lips with the speech, but the audio is never heard. This audio problem only occurs in Free Play mode.
Bug: Rapturous Rise: Around the point of the level where the dinosaurs show up, The Thing will pick up a massive boulder, either intentionally or unintentionally. If you switch to then play The Thing, the Boulder will remain in his arms and his character to cannot be switched to the opposing character nor can he change his character when played in Free Play. This bug only occurs when Rapturous Rise is played in Free Play mode.
Continuity mistake: Taking Liberties: Partway through the level, The Hulk, Mr. Fantastic and Wolverine will have to go into a lift. When the lift reaches the second level, all of the positions of each person in the lift have been reversed. They are completely different to when they entered.
Bug: That Sinking Feeling: When Iron Man, Spider-Man and Thor are battling M.O.D.O.K., after he has lost two lives and you have battled all of the guards, he will fall to the ground for someone to hit him. If M.O.D.O.K. lands on the left hand side of the platform and it is Thor who is hitting him, M.O.D.O.K. still won't lose a life.
Continuity mistake: After completing "Juggernauts and Crosses", it will show the Fantastic Four outside Baxter Building. The Thing and The Human Torch will then run off, leaving Mr. Fantastic and the Invisible Woman. The two will then go to Central Park and get in the Fantastic Car. When they get into the shuttle, it is still just them, but when the intro clip for "Doctor In The House" starts, The Thing, The Human Torch and Nick Fury have appeared in the shuttle from nowhere.
Bug: Rebooted, Resuited: There is one point in the level where Captain America and Iron Man need to open a laser gate with three blue lasers along it around the second area, in which it asks you to save the level at the checkpoint for the first time in the level. If you continue to the right, you will be able to jump onto a blue and white striped climbing wall, climb up it, and at the bottom of the wall is an electric pit. If you attempt to climb the wall and you miss the wall, you fall into the pit. When you are in the electric pit, if you push the button to switch characters, it won't let you switch characters at all.
Bug: Exploratory Laboratory: Just before the clip of Black Widow, Hawkeye and Spider-Man plummeting into the lower level is shown, Spider-Man has to launch a web at a web target above him. If you launch the web whilst you are directly under the target, Spider-Man will get stuck in the target.
Revealing mistake: Baxter Building: After letting Captain America out of the park gate and Captain America breaks the Shield Switch on the wall with his shield, a ladder will drop. If you climb the ladder, the shadow of an air conditioner instantly appears on screen. There is no air conditioner as you start to climb.
Factual error: Baxter Building: The position of the lock on the park gate outside Baxter Building is in a completely impossible position. The key hole part of the lock is located inside the interior of the park instead of the exterior where the gate is usually locked from. There is no reason the key hole part of the lock should be located inside the park.