The Friendly Physician - S2-E29
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: 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.
Santa Comes to Visit and Stays and Stays - S6-E14
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)