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.
Plot hole: In this film the aliens are said to be operating with a hive mind, and are all telepathically linked to the alien queen on the mothership. It is also stated the mothership from the first film also had a queen that was never seen. If that is the case, then there would not have been any need in the first film to use Earth's satellites to coordinate the attack.