Japan never developed one man submarines, and even if it had, it would have run out of fuel long ago.
The captured castaways are held in bamboo cages, supposedly booby trapped with grenades that would explode if the bars where pried apart. However, the grenades are clearly just hanging from wires like Christmas tree ornaments. Also the grenades are within easy reach, and potentially could have been taken by the prisoners to use against their captor. Furthermore, Japanese WW II grenades did not function as portrayed. Simply pulling the pin would not arm the grenade.
As the sub is going down with Gilligan in it, water inside the sub is rising at the same level as the water outside, making it obvious it is just the top of a sub prop.
The Japanese Sailor mentions Lloyd Bridges as being a famous movie star from before 1942. But Bridges was primarily cast in unbilled or minor parts, and didn't become a star until well past the end of World War II.
When the periscope of the supposedly submerged submarine being piloted by Gilligan is running circles in the lagoon, a scuba diver's air tank rises above the water just behind it.
The Japanese man has apparently been on the island since 1942, but somehow never met Wrongway Feldman (or Dubov the painter, or the jungle boy) who was already living there.