In the Xbox 360, PlayStation 3 and PC versions of the game, the boss fight with the Blob is set in a grocery store, as opposed to the Wii, PlayStation 2 and PlayStation Vita versions being set in a boxing ring, much like the film. This is because Raven Software used an earlier version of the movie's script written by David Benioff & Skip Woods, rather than the final script used for the movie.

For the Xbox 360, PlayStation 3 and PC versions developed by Raven Software, it was decided early on in development that the game's combat would be bloody and visceral. Raven wanted the gore to be realistic, but not too over-the-top where it felt excessive. However, considering this was a tie-in for a movie aimed at a more general audience, giving the game a Mature rating was an uphill battle. One of the earliest gorey sequences produced and shown to Marvel and Activision was the scene where Wolverine grabs a pilot and lifts him up into a helicopter blade, decapitating him. The reaction from all parties, including Raven themselves, was shock, but the vertical slice was so well received that it ensured the game would receive a Mature rating.

In chapter 3, it's possible to find a teleporter that will guide you to a room with a cake in it. On the wall is the word "surprise!" written multiple times. Finding this room will unlock the achievement "The Cake". This is a reference to Portal.

In chapter 2 is a hidden cave. Within the cave is a sword sticking out of the ground next to a skeleton with an exclamation mark above its head. Finding this will unlock the achievement "WoW!" This is a reference to World of Warcraft.

Soon after crashing the 4x4 in chapter 1, it's possible to find a hatch hidden in the ground. Standing over the hatch for a short period of time will unlock the achievement "Found!" This is a direct reference to the TV series "Lost".