(at around 47 mins) When Brian first looks at the Earth (from outer space), it is a mirror image (Spain on the right, Middle East on the left). In the next shot it is a normal image.
Indira says at the beginning the spaceship is moving "very fast". Even assuming that was only about as fast as an average asteroid, that means dozens of kilometers per second. Even launching the missiles at a distance of 10,000 km would mean cutting it very fine, with just a few minutes to impact. Waiting until the ship went through the atmosphere would leave mere seconds to its impact on the ground.
At 34:55, when Solomon takes Queen Nefertiti back to his ship, the computer says "hostile targeting in progress", while the screens say "hostile targeting in process".