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: "The Phantom Strikes": The Seaview's crew have a wild shootout aboard ship, and their bullets are seen to go all the way through a 6-inch-thick hatch door. Gee, you'd think that somewhere during their military training, somebody would have taught these guys why firing high velocity weapons on a submerged submarine is a really bad idea. (00:38:15)