Plot hole: Gilligan admits he put the Professor's measuring stick in deeper and deeper waters to catch bigger lobster. So wouldn't the Professor have noticed the stick has been moved further out (and more than once too) in the water rather than think the island is sinking? He always had all positions and locations down to a science in many episodes, so how could this have gotten past him?
Continuity mistake: The professor mentions he can't drink vodka with the Russians because he's allergic to alcohol, yet in the episode "Man With A Net" (with Lord Beesley), he drinks a strong alchoholic drink he made along with everyone else with no signs of any sickness, or reaction preventing him from drinking it.
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.
Visible crew/equipment: Toward the end, the group is around the table, talking about Gilligan. Then they see a pear and a bunch of grapes float over to a plate at the head of the table. Skipper goes over and addresses the invisible Gilligan. If you look at the top of the hut, you can see the wires used to make the fruit float. Also, earlier in the hut with Ginger, when Gilligan bit the pear, you can see the wire holding the pear as it shakes after the bite.