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 scientist yells for Igor to capture the escaping Castaways, to which Igor responds "capture them yourself" in Ginger's voice. The scientist appears surprised to find out Igor is not Igor, but how can this be? He had to be the one to pull the lever to switch everyone's personalities and bodies around, so he should have already known.
Plot hole: Solo blows open the ceiling vent of Illya and Marion's cell, and she stands on Illya's shoulders until Solo can reach her and pull her out. This leaves Illya with nothing/no one to stand on, no way to reach the vent and no apparent way out of the cell. But he's out just the same in the next scene, with no explanation as to how. (00:42:40)
Plot hole: Mrs. Kravitz, while standing in the Stephenses' front doorway, sees Santa Claus and assumes that it's Darrin in costume. However, the very next shot shows Santa exiting the kitchen (around the corner from the front door) and starting up the hallway toward the living room. There is no possible way Mrs. Kravitz could have seen him when she said she did. (00:09:30)
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)
Plot hole: Dr. Quest is speaking through the Dragonfly's speakers to the Po-Hos as they fly over the jungle, telling them he is their air God and is angry the tribe has taken hostages. Quest could have told the Po-Hos to just release the hostages, rather than putting himself in danger later on by getting captured.