At the beginning of the Facility level, players are required to open a door with a computer switch in order to progress to the next area. Unfortunately, the computer can be destroyed, leaving players stuck in the starting area. In order to get around this, the developers added a scientist that eventually rushes to the bathroom. He is carrying keycard A, which will open all of the doors in the level (with the exception of the bottling room, which requires the door decoder).

There are several small guard towers found throughout both Surface levels. Despite having guards armed with sniper rifles, none of them are placed on these towers. The reason why the towers aren't utilized has to do with how the game handles guards' line of sight and gunfire. Guards can only see Bond if they have a clear line of sight to him across collision tiles. Since the towers' collision tiles only connect to the ground's tiles at their ladders, the only place guards could actually see Bond is when he was standing in front of the ladder. Even if sight was faked, as the game does elsewhere, bullets work in the same way as line-of-sight and will be blocked by the collision tiles. Both of these limitations combined would have rendered any snipers on the towers completely ineffective. The towers were kept in the game merely for decoration and completeness.

In the Dam level, there is a blue metal trapdoor on the floor in a guardhouse that serves no purpose in the final game. Many believe it was part of an older objective that was taken out of the game. Some speculate that Bond previously had to retrieve his tracker bug for the mission in this hatch, since the message "Picked up a bug" can be found in the game's memory but is never used in the game. Others speculate Bond previously picked up explosives here for a lost objective requiring players to blow up the truck. Still others believe it was merely a quicker way to the comms room below the dam, since it is almost directly above it. It's true purpose remains a mystery.

The Statue and Cradle levels were once both playable multiplayer levels, but were taken out of the final game. Both can be accessed and played with a GameShark, and both levels contain weapons, ammo, and body armor. However, Cradle had severe lag issues, especially with more than two players. Statue also suffered from frame rate issues and contained several glitched areas that would not load properly and turn black. It was likely these levels were both taken out for these reasons.

The runway level was originally supposed to include a controllable motorbike, similar to the movie. However, no motorbike appears in the final version of the game. It was likely scrapped before the release due to the difficulty of controlling the bike in a first person shooter. A miniature model of the bike was ultimately placed on a desk in one of the huts on Surface as pure decoration. A life size model of the bike also still exists in the game's memory and is accessible through codes.

In the dam level, there are three guard towers on the main dam, and one across the lake on the hidden island. The ones on the dam are marked 2, 3, and 4 in order, and the one on the island doesn't have a number. This leaves guard tower 1 missing from the game.

It's possible that this tower originally appeared immediately to the right of the locked gate to the dam. When it was eventually removed, the developers may have simply forgotten to change the other numbers.

Even after unlocking all 23 cheat options through the single player campaign, there is still an empty 24th space left in the cheat menu. This space is left for nine cheat options which cannot be unlocked during the course of the game. They can only be added to the menu using a GameShark. The cheat options include:

Extra Characters (800696XX 0001)
Maximum Ammo (80069654 0001)
Line Mode (80069657 0001)
Super 2X Health (80069658 0001)
Super 2X Armor (80069659 0001)
Extra Weapons (8006965D 0001)
Super 10X Health (80069660 0001)
Multiplayer Invisibility (80069666 0001)
Debug Position Display (80069669 0001)

Several of these cheats can also be activated by button codes in-game.

The GoldenEye 007 instruction booklet lists a Soviet weapon called the Spyder. However, no weapon by the name of the Spyder is found in the final game. The name Spyder was actually dropped due to legal reasons, and the gun was renamed the Klobb after Nintendo of America's Ken Lobb, who helped the game during its development. The manual was simply printed without the correction made, or it was printed before the name change took place. Before being named the Spyder, the gun was also called the Skorpion, based on its real-world counterpart, the Skorpion VZ/61.

In the Frigate level, there is a locked door on each side of the ship's bridge. They are impossible to get trough without a GameShark and only lead to a small balcony overlooking the ship's deck. Why they were left in the game (or what purpose they could have once possibly served) is unclear.

In the first Bunker level, there is a Russian commandant who carries a PP7 special issue. He is the only commandant in the game who carries a PP7 - all the others carry DD44s.

David Doak, a video game developer who once worked for Rare, was part of the Goldeneye 007 development team. He was rendered into the game as Dr. Doak in the 2nd mission.

There are actually several floating doors in the Frigate level that are accessible if you perform a few glitches. The doors are left over from when the developers decided to turn them into doorways, but chose not to delete the doors for some reason. They still exist in the level's geometry, but only from certain angles.

In order to see them, turn on Tiny Bond from the cheat menu, and head for the first set of stairs heading down to the engine room. If you do the floating Tiny Bond glitch (crouch with R and C-Down) and walk down the stairs, you'll float over them and into the geometry of the level. Eventually you will see a door floating in space. If you open this door in mid air, go through it, and turn right, you will see a second door floating in mid-air as well. You cannot reach the second door without falling down, however.

If you plant remote mines on the floating doors, then go back around to the hallway and detonate the mines, they'll explode in front of you without any visible fireball. The explosion will merely send bits and pieces of debris flying everywhere.

Fully-textured models of Timothy Dalton, Sean Connery and Roger Moore are all hidden in the game's code. They can be accessed via cheat codes, but only in the game's menus.

The code of the game hides a working ZX Spectrum emulator. A Rare developer, Steve Ellis, coded it simply to see if it was possible.

In the first level of the game, the Dam, there's a small island near the end which can be seen from afar. The island features a guard tower and an inoperable drone gun with some beta textures. It can only be reachable using a cheat device and a no clipping cheat enabled.

Left over code suggest the player had to travel to the island and retrieve proper equipment to perform a bungee jump. 'Piton Gun' and 'Bungee' can still be seen in the games code, and a Piton Gun is what Bond used in the movie to get to the facility. However, according to Duncan Botwood, one of the developers on the game, it was originally planned for players to investigate the area and find some armor as a reward.

There's a hidden test level called "Citadel" found in the game's coding. It was designed during the early stages of multiplayer and had it been functional in the finished game, Oddjob and Mayday wouldn't have been available to play.

The level can only be accessed through the use of a cheat device. As an obvious test level, however, there are numerous glitches which prevent it from being properly playable.

At one point in GoldenEye's development, reloading your weapon was going to be triggered by removing and reinserting the N64 Rumble Pack as if you were removing a magazine on a gun.

In the Xbox One version of GoldenEye 007, the DK Mode - named after Donkey Kong for changing the proportions of in-game models to those of DK's from Donkey Kong 64 - retains its name. Given that Nintendo were directly involved in the project to re-release GoldenEye 007, with the game having a simultaneous relaunch on Nintendo Switch Online and Microsoft Store, this could be the first time Nintendo has officially allowed their IP to be referenced on a direct rival console.

A common debate among GoldenEye 007 fans is whether playing as Oddjob in the multiplayer mode is cheating due to his short stature going below the auto-aim bullet radius. This would be addressed by lead environmental artist Karl Hilton and gameplay and engine programmer Mark Edmonds in an oral history article released by Mel Magazine in 2018, 21 years after the game released, who stated that they too thought playing as Oddjob was cheating, and they were aware of this during development:

Censored Gaming asked director Martin Hollis why the Hunting Knife was removed from the Japanese localization. He stated that it was related to the Kobe child murders, a pair of highly publicized 1997 child murders carried out by a 14-year-old boy. This change is believed to have affected Rare's later game Perfect Dark for the same reason.