There was originally going to be fights against both the Infantry General and the Demolitions General in the Zero Hour expansion. Both of these fights are still in the game but cannot be accessed through normal gameplay.

There are quite a few unused mouse cursors left hidden in the game's memory:
• Defector - Intended for the removed Defector special power.
• Guard - An unused unique cursor for the Guard function.
• Heal - Could have been intended for the Ambulance, or perhaps used when you send injured soldiers to the barracks.
• No Entry - Shown when you cannot enter a building. In the final game, the standard "invalid" cursor is shown instead.
• Out of Range - Intended to appear when you tell a unit to attack an enemy unit that is not within range.
• Place - Would have been used as a cursor when you place a structure.
• Sell - Sell does not require a target in the final game, as all structures have sell buttons to sell themselves.
• Spy Drone - An unused unique mouse cursor for the spy drone feature.

Some of the special powers were removed from the final game due to the fact the developers removed the generals feature in the base game (this was later re-added in the expansion). However, their code still resides in the game's memory:
• Black Market Nuke - A GLA special power that sends a plane to drop a nuclear bomb.
• Terror Cell - Similar to the Rebel Ambush feature that made it into the game, except this spawns terrorists instead of rebels.
• Crate Drop - Does nothing more than drop $2,000 worth of money.