The jungle boy has been on the island all this time, but does not have long unkempt hair.
When Gilligan is inside the balloon trying to retrieve his hat, the inside can be seen to be smoother than it would be if made of raincoats.
If the buoyant gas was hydrogen and/or helium, Gilligan's voice would've been higher pitched after he stuck his head over the gas vent and breathed it in.
When Gilligan climbs into the balloon to retrieve his hat that has floated into it, he would've suffocated, since all the oxygen would've been displaced by the buoyant gas.
Whenever a person or object is lifted up by the helium blasts from the mound, support wires are visible.
When Jungle Boy swings through the air on a vine, it is apparent that it is an adult stuntman, and not an adolescent boy.
When Gillian tries to swing on the rope to follow Jungle Boy, it's obvious that his "vine" is a rope covered with camouflage.
With proper teaching, the jungle boy would have learned how to communicate well enough to tell of the island and castaways. It would have taken a few months.
When Gilligan tries to tell the others about the jungle boy, the Professor claims that he's previously searched the whole island, declaring there's nobody else here. Later in the season, they'll finally run into Dubov, who was on the island before the castaways.