When the speedboat is going through rough seas, it is clear that a good deal of water is being shipped aboard the vessel. However, when we see the cabin, with the entrance open to the seas, there is no water whatsoever coming down inside.
After Howard Thomas sees his wife in the jacuzzi, his glass has some alcohol left in the bottom. When it cuts to the glass dropping it is clearly empty before smashing.
The car Howard Thomas drives is a Volvo 740, but in some scenes it is a pre-1990 model, while in others it is a 1990 model or newer.
When the sub is unstuck from being "bow first" in the rock face, it is in full reverse. In the next shot, it is suddenly going forward.
In Florida the vehicles only have license plates on the rear of the car, however all the vehicles shown have them on the front.
When Dr. Geller is looking at the obits, the birth and death dates do not match up with the text. Furthermore they are in the day/month style which in the US is only common for military publications, not a paper in Miami.
Car dive sequence into the sea after the bridge disappears, you can see cable on both sides of the car holding it somewhat at an angle as the characters are trying to get out of danger. It shows both times the accident happens at two different time warp occurrences.
In an opening title, the Sargasso Sea is described as being in the South Atlantic Ocean. It is in the North Atlantic.
It is claimed that the Atlantic is the deepest ocean when the deepest ocean on earth is actually the Pacific.
When entering the sub for the first time in part one, Emily Patterson says that she thought that Lithuania was land-locked. It is located on the Baltic Sea.
Just before boarding the submarine, Emily Patterson recognizes it as Soviet-built Foxtrot class. Later it is possible to see that the sub has two three-bladed propellers. In fact, Foxtrot class submarines had three six-bladed propellers.