The aircraft on the tarmac at the beginning of the episode is an Airbus A320. Once airborne with the Doctor and TARDIS aboard, it is depicted as a Boeing 737.
When The Doctor approaches the pyramid the first time, the sun appears to be behind the Doctor on his left because his shadow and the pyramid's shadow are going to the right. When he reaches the pyramid and is talking to the alien, the sun is illuminating the Doctor's right side and the alien's left side. When the camera changes to show the view from behind the alien, the Doctor's left side is illuminated by the sun.
The character of U.S. "Colonel" Brabbit is actually wearing General's rank insignia.
There are a multitude of ways to accomplish sterilization, but the ones mentioned by Erica are among the least effective. A scientist would suggest chemical, autoclave (high heat steam), pressure, or irradiation before suggesting dropping something into boiling water.