Plot hole: The Mighty Atom is only supposed to take pictures of human faces yet we see it taking photos of the machinery in the Saharan Plant when no one is in the room.
Plot hole: When Jeff Tracy contacts Lady Penelope, it is 10:00am in England, yet it is already daylight on Tracy Island in the South Pacific and Alan, Gordon and Tin-Tin have been out fishing for some time. (It is later established in the 1966 "spin off" movie "Thunderbirds Are Go" that there is a five hour time difference between Tracy Island and England. So, using that as a guide, when it's 10am in England, it should be 5am on Tracey Island.)
Pit of Peril - S1-E2
Plot hole: The Sidewinder was heating up all the time and it was becoming increasingly uncomfortable for the crew men inside, yet none of them thought to take off their thick jackets.