On board the Sea Grass Nick tells Elizabeth the story of how his father found a "Gold Doubloon, minted in Spain, 1867," on another ghost ship. However, the last Gold Doubloons minted in Spain were in 1849.
Elizabeth takes off her gloves when she first gets into Nick's truck near the beginning of the film. When the windshield shatters and Nick is struggling to control the truck, she is wearing the gloves again in a few very quick shots.
When Nick and Elizabeth go to the dock to meet The Seagrass the weather is overcast and looks like its going to rain. In the very next shot we see Mrs Williams and her assistant organizing the 100th anniversary of Antonio Bay and it is clear blue skies and looks very much like a summer day.
When Sandy and Mrs. Williams are driving to see Father Malone, it is sunny and clear outside. As they drive up a hill, the day is suddenly cloudy. Then, when they arrive at the church it is sunny and clear again.
When Nick & the group are at the church near the end of the film, Nick grabs Father Malone's whiskey bottle and smashes it. Whiskey is shown soaking one of the pews. A few minutes later, the same pew is shown again and the pew is perfectly dry. The amount of broken glass has changed as well.
A Ford Country squire station wagon has its headlight doors open, which would be true if the lights were on, but they are not. For no apparent reason, in the next scene, the headlight doors are closed.
When Nick (at the bar) is on the phone with Stevie telling her about the SeaGrass, there is a cutaway to the lighthouse. To the left you can see a crew member motioning for more fog, and then more fog rolls by him.
In a few scenes, Dan the local weatherman is tracking the fog bank on his weather radar, and giving reports. Weather radars have never been able to detect fog. Today's most powerful state-of-the-art NEXRAD radars are sensitive enough to detect bugs, birds, and smoke plumes, but still not fog.
Antonio Bay is set in California, the West Coast, but throughout the movie characters reference the fog as moving west, toward the town - sometimes against a due east wind. That would mean the fog was actually moving away from the coast, not toward it.
As the ghosts break through the windows in the church, some of the mutton bars break away but not the glass between them. Instead of being made up of separate panes as those of that period would be, they seem to be solid sheets.
When Elizabeth & Nick are riding along in the truck after he first picks her up, we see the glass in the windows begin to smash inward. One can briefly see the object used to break the glass before each smash.
When Stevie brings the piece of the ship The Elizabeth Dane to work, it begins to leak water toward her cassette recorder and the recorded voice slows down. But the recording begins to slow down before the water even touches the machine.