Plot hole: The creature gets caught in the fishing net and (after a struggle that shook the whole boat) freed itself. The scientists, upon drawing up the net, find one of the creature's claws, and thus they now seek its source. Shortly after, while Mark is busy loading a harpoon gun, Dave is protesting, stating, "This...this thing *alive* and in it's natural habitat..." It would seem that at this point, they know the creature is *not* dead, but very much alive. They dive, they see it, Mark shoots it with a harpoon, and then upon surfacing, they argue a bit before reporting what they saw to everyone else. So why after seeing it underwater, fully knowing that "this thing (is) alive," do they act so surprised to see it, as if they didn't have a clue it could possibly still exist?
Plot hole: In the scene for Heihachi's funeral: Gisaku is at the funeral and is seen full face as Kikuchiyo shouts the bandits are coming. Everyone runs for their posts and bent over Gisaku is left standing by the grave. Kikuchiyo runs to dismantle the bridge with his crew when Gisaku's son, his wife and baby come by to get the old man who they say has refused to leave the mill. There is no way Gisaku could have outrun Kikuchiyo to the bridge and there is no way that his son and daughter-in-law could have known he was in the mill"
Plot hole: Helena is ordered to fly or be thrown off the tower, bearing the brunt for Simon's failure. But the flying apparatus is still up there, and so is her servant who was going to secretly operate it so that Simon could pretend to fly around. All she needs is right there in front of her. She's supposed to be cunning and resourceful, and she could have saved her life simply by following the original plan.
Plot hole: The Thorwalds were supposed to be in the apartment for only six months according to the lease, their phone number wouldn't have been published in the phone book for such a short lease.