At the end of the movie, Gus is completely dry despite having been underwater only a few minutes earlier.
When Merrick examines the chemicals container on the shipwreck it remains bright inside even after he removes the flashlight.
During the chase in the woods, the right front hubcap comes off of the Dodge, but it's back in the next shot.
When Dan and Gus arrive at the ship near the end of the film, it is pouring rain but a closeup of Tom Berenger clearly shows that neither actor is getting wet.
The initial car crash ostensibly happened in Marin County CA, but a scene where they return to the crash site shows granite talus slopes and tall pine trees, as found in the Sierras or Rockies.
An asthma inhaler is not an aqualung. Klein could not have kept breathing underwater because he had his inhaler with him. It relies on mixing the steroids with the surrounding air; it doesn't itself provide oxygen.