Two pieces of game footage that play during the end credits contain material that don't actually appear in the main game. First, the baby frogs don't burst when Frogger approaches them. Second, the barrels from the Sewer Zone don't explode when hopped on. It's possible that the footage was recorded before these features were removed later in development.

In the PC version, the Hasbro logo plays as normal, albeit the ending shows the "Escape" video compression logo. However, in the PS1 version, the logo is somewhat out of sync, resulting in both the audio getting cut off at the end, and the "Escape" logo not being shown.

The frog's in-game models appear to be completely different in both single-player and multiplayer modes.

A demo build of the game shows that Frogger would've had a lot more animations, including Frogger bouncing, doing a mid-air flip, and extra death animation, hopping to his left and right, doing a cartwheel, a "leapfrog" animation, panting, an alternate slipping animation with one slipping to the left and one to the right, a drowning animation, doing a super hop, two idle animations, kicking upwards while doing a handstand, and doing a "superstart."

The sinking and mid-air flip animations would later be used in the sequel.

According to lead programmer Tim Closs in a 2015 interview with the franchise fansite Highway Frogs, Frogger was supposed to be an open-world 3D game (in a similar vein to Super Mario 64, which released a year prior). Internal disagreements caused them to change it to operate like the original Frogger game, but in a top-down 3D style.

The expansive maps, outside of the Retro Zone stages, may be a remnant of this original idea.