Enemy NPCs all differ substantially from their canon counterparts.
The inside of the Republic assault ship's bridge does not match the outside.
At the beginning of the first mission, Republic AT-TEs and Homing Spider Droids are shown in close proximity, yet the Homing Spider Droids are facing away from the AT-TEs.
Even though their helmets are supposed to be sealed, the Commandos state several times that they can smell things.
In the anti-aircraft bunker on Geonosis, there is the body of a clone soldier, even though there is no way that it could have gotten there.
The Trandoshan jamming device on the bridge of the Republic assault ship needs to be destroyed by explosive, which sent a good idea since it is near the bridge windows.
Delta Seven states that he can see a Trade Federation battleship at the edge of the system. It is impossible to see very far in space.
Delta 62 acts like he has not seen the anti-armour attachment, even though he had to have trained with it already.
Delta 38 states that he didn't think that anyone used projectile weapons anymore. Considering that he is a commando, he should have been briefed on a wide variety of weapons used by other factions.
After using a holoprojector to contact the Advisor, the commandos never pick it up afterwards.
The captain of the assault ship sent to assist the one the commandos are on asks why the guns are not working. Since most guns in the universe of Star Wars require crew, it should be no surprise to him that they are not firing.
In the final mission, the turrets being used to fire upon the Separatist ship are called both rocket turrets and turbolaser turrets. They are, in fact, turbolaser turrets.