
Continuity mistake: When General Grey tells the President not to engage until they have visual, in the President's close-up the exterior of this F/A-18 Hornet is quite different than what was shown in the earlier shot, as the canopy closed over him. All the rivets around the canopy have disappeared and the 'danger' triangle is much closer to the name Patrick, the seat differs, etc. Plus the fact that the canopy and hull are actually one unit in the second shot. (02:02:15 - 02:03:15)
Answer: Remember that the aliens had to interface with our satellite computer code first...David simply "reverse engineered" the code to create the virus. When it was uploaded, they didn't have enough time to combat it.