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.
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.
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.
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.