Jeff states that he wants Scott to take Alan up to Thunderbird 5 to relieve John. It is unclear why Scott would have to do this since Alan and John are the primary pilots of Thunderbird 3. Additionally, Scott does not even go up to the flight deck (where the flight controls are) with Alan. He remains on the lower deck.
After his trip up to Thunderbird 5 taking Alan up and bringing John down, Scott comes up from the launch bay alone on the couch/elevator. John should be beside him.
Thunderbird 1 takes a direct hit from a missile fired by one of the Zombite fighter planes. Brains later mentions that he repaired the damaged radio, but makes no mention of the damage done to the ship itself by the missile impact.
Puppet strings range from being slightly visible to patently obvious. Thunderbirds is a puppet show. They're not meant to be special effects. They're not trying to hide the strings.
Double-Z Zombite logo is backwards in one frame, revealing the usage of a mirror image.
As Tin-Tin reacts to Scott's disappearance, a floor puppeteer's hand can be seen lifting her from her seat.
It is unclear why Scott flew over the Sahara on his way from Tokyo to Tracy Island (described as being in the Pacific Ocean), as doing so would have added approximately 10,000 miles to his journey.