Continuity mistake: At the end of the movie when the mothership takes off the central saucer section is in place, yet we saw the queen alien fly off in it earlier on.
Continuity mistake: Early in the film, as Jake and Charlie are towing a new weapon system to its destination on the Moon, we see Earth in the background, more than half illuminated by the Sun. Jake says they are 7 miles away and closing on their lunar destination (which should only take a matter of moments). A few moments later, as Jake and Charlie are still in approach, we see Earth in the background again, but it is now in a waning crescent, only 1/3 illuminated by the Sun. This would indicate over a week's passage of time.