When Gilligan runs out of the cave, his hat falls off. In the next shot, the hat is back on his head, even though he has clearly not stopped to pick it up.
The island seen out the search plane's windows is clearly different from the one seen in other installments.
After the murder scene play, The Professor is laying on Ginger's bed with a bloody nose. And his head is tipped back, in real life blood can drip down your throat causing you to choke.
The phosphorescent rocks are never mentioned again as a possible rescue aid.
When Gilligan stamps out the fire on the sand, the ground bounces up and down because there is obviously a mat underneath it.