In the cut scene before the Felucia: Heart of Darkness level, Aayla Secura has a blue and a purple lightsaber, but during gameplay, she has a blue and green lightsaber.
During the space fight scenes, two targets on the enemy vessel are the Communications Array and the Sensor Relay. However, when the voice of your commander refers to them he says the Communications Relay and the Sensor Array, mixing the two up.
The clone troopers hold weapons in their right hand (with their left to steady two-handed weapons), meaning they are right handed, but on the cover of the game case, the trooper has the gun in his left hand. If all of the troopers were cloned from Jango Fett, they would all be right handed.