To meet deadlines The Collective had to cut a lot of content out of the game. At one point Indiana was going to have two whips, one of them being a magic grappling hook.
According to the unlockable artwork, the character Abner Ravenwood (Indiana's mentor and father to Marion Ravenwood) was originally to make an appearance in the game, but had to be cut.
There are two training levels in the PC version of the game not found in the console version.
In the Prague levels, while you're batteling the Gestapo agents, one of them shout "schießen aus dem Fenster" which in German means "shoot the glass" this is an obvious reference to Die Hard (1988)
Also planned was a level involving Indiana being chased from boat to boat. Due to time constraints and the amount of technology that had to be written to accommodate the level, it had to be cut.