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.
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.)
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: In order to build up suspense, Virgil and Brains stand on the Crab Logger as its dangerous fuel is pumped out, despite the fact that it is hanging on the edge of a precipice. In fact they could have left as soon as they had plumbed in the pipes to empty the fuel tanks - the whole procedure is controlled by Scott in Thunderbird 1 and they make absolutely no contribution to the operation at all. They do not need to disconnect the pipes; they are left behind and dropped from Thunderbird 1 as planned. They just stand there chatting about how much danger they are in until jumping clear at the very last second. Silly buggers.
Plot hole: Crablogger designer Jim Lucas lives at 75 Sunnigale Road, Eppington Wood East, Somerset, according to the card that Penelope finds in the personnel files at Robotics International, but she reads it out to Parker as "20 Hazlemere Gardens, Iresham."
Give or Take a Million - S2-E6
Plot hole: It is supposed to be the middle of the night when Virgil sets off in Thunderbird 2 for Coralville Hospital, but the Thunderbird 2 launch takes place in full daylight.