On "What if?" mode, the Ark of the Covenant can be found inside a crate at the beginning of the level "Waterfront Warehouse". This could possibly be a reference to Raiders of the Lost Ark, in which the Ark of the Covenant is sealed in a wooden crate and stored in a government warehouse.

The game's executable file contains developer comments about frustrations of coding the game and comments about being angry with one of the developers.

Entering a variety of curse words or inappropriate words on the game's cheat menu will cause Spider-Man to appear and alter the entry into something nice instead by punching it.

At the starting point of the "Race to the Bugle" level, Ghost Rider can be very briefly seen riding down a building before disappearing. This cameo is an exception to the other Marvel cameos in the game's "What If" mode, as Ghost Rider also appears in the normal level.

During the third Speed Training level, a metal door on top of a building can be shot at to open it, revealing a hidden group photo of several Neversoft developers behind it. However, it appears that there are at least two different developer photos that can be found behind this door. It's unknown if the appearance of each photo differs by the version of the game being played, or if one is randomly selected when the level is loaded up. This building is located diagonally across from a building with a billboard for Tony Hawk's Pro Skater 2 on it, which was also developed by Neversoft and released the same year as this game. This Easter egg went undiscovered until 2021.