In the scene where Crasher insists on going after Leader-1 her face around her eyes appears to be almost banana yellow instead of peach.
In the scene where Rest-Q is trying to figure out why Small Foot can't convert her chest plate is seen opened and her insides are exposed. In the scene after Matt asks if Rest-Q can put Small Foot through to modifier for a second time the camera is panned out and her chest plate is seen reattached.
The Last Engineer's ship "Courageous" is green not the standard red, white, and royal blue.