You need to work out the lighting more on the composite shots. The original plate and the composite shot dont match. The composites are too bright and they contrast heavily against the original plate. Try lowering the brightness on the composites and throw in an alpha layer of haze. Notice all the haze in that first shot. The speed of the ships doesn't match the speed of the plate either. The people are running in slow motion while the ships seem to be moving at normal speed. Also there are two ships - one is closer to the camera than the other, yet they are both still the same size.

I'm seeing a thin black line around the ships in the first shot. Are you color keying them in from a black background? Dont! Use Alpha Channel. You wont get that thin black line.

Oh, and on a funny note...

If that guy gets vaporized, why is he in the goup when they run back the other way?