In the final scene, Caine and JJ are on top of Sears tower, presumably having flown up there with wings and anti-gravity roller skates. No police or military or news or civilian involvement so far. Then they start flying AGAIN in broad daylight, unconcerned that someone might see them.
Also, was there any good reason JJ needed to be on the Abrasax ship when going to visit Balem? Why would she consent to that? How did the crack team of space guardians, hell-bent of protecting JJ, not see it coming when the bad guys basically CLOSED THE DOOR before they could enter?
Also, Balem had tens of thousands of years to build a harvesting factory on Jupiter, but it was designed in such a way that the ENTIRE massive thing explodes and crumbles if a space ship crashes into ONE part of it.
Why are the light elevators so damn slow?