When Rae tells Hughie to get the canopy down, he shuts the door and we see Rae through a mirror while she gets the shotgun; the camera is briefly visible in the mirror before quickly moving out of sight.
After Hughie captures the yacht, John rows back to the schooner. Halfway the movie the row-boat is still visible tied behind the schooner. Yet, as the schooner is sinking, John escapes by a raft. Why didn't he use the row-boat?
In the final scene where Sam Neil shoots Billy Zane through the sail with a flare you can tell by the shadow of Zane that his head is faced sideways. The flare goes into Zane's mouth however killing him which can only mean Zane was facing Neil when he fired the flare at him.
The goof items below may give away important plot points.
When John is trapped in the sinking boat and has to resort to using the pipe to breathe, it's clearly visible that there is no air at all in the room he's in. When he notices a fish got into the room, you can see air pockets in the ceiling.
When Rae is at the helm of the boat after she had tied Hughie up she is wearing make up in the shot before she was not. As the scenes changes between John drowning and her steering she gradually has more make up.
On several occasions, namely when John is pounding on the hatch after he runs out of air when trapped inside the ship, and when he swims out, we can see water running out of the ship above the water line. This couldn't happen if unless water was being pumped into the ship, or it was being hoisted out of the water, which we know it wasn't.