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.
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.
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.