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.)
Deliberate mistake: Throughout Thunderbirds, when the script required objects to be manipulated, there were cutways to close up 'insert' shots of real human hands - usually of the puppeteers/crew. However in this episode, Alan's close-up (i.e. live action) hand is remarkably hairy with very dark hair. Yet Alan Tracey is supposed to be 21 and blond haired (including the hair on the back of his hands).
Other mistake: As Virgil prepares to clear the wreckage of the tower from the rescue area using the Firefly, Scott tells him that he will go over to Thunderbird 2 to prepare the Mole for tunneling. The Tower Controller then says to Scott, "I've got a fast car ready for you outside" without moving his lips.
Continuity mistake: When the door of Pod 1 opens after Jeff realises there is a saboteur on board, we see three vehicles in the pod and beside the Monobrake there is a red unit which has a windshield on it. However, when we see Chip appearing in the next shot, the windshield has gone.
Continuity mistake: Watch the time on the clock on the wall in the USN Sentinel during the missile attack. At the start of the attack it's 12.45pm, but later on it changes to 1.05pm, and when Washington informs the Sentinel Commander to stop the attack, it's now 1.35pm.
Continuity mistake: When Virgil is seating at the cockpit during the launch sequence of Thunderbird 2, he is wearing the clothes he wears on Tracy Island and his International Rescue costume appears. But when Alan comes down the lift, Virgil has suddenly changed into his IR costume.
Continuity mistake: During the missile attack on Thunderbird 2, Virgil says "Missiles!" in the cockpit and his forehead can be seen to have sweat on it, but after a quick shot of the missiles flying through the air, we cut to Virgil again and the sweat has disappeared.