Revealing mistake: When one of the bad guys is being dragged around by the monsters and thrown against pipes and walls and such, in wide shots you can see there is no monster really pulling him, and from the stiffness and position of his body, he is likely on some sort of device to swing him around.
Revealing mistake: Occasionally, when the characters are being eaten by the sea-monsters, you can see pieces of the computer-generated beasts going "through" the victim.
Revealing mistake: When Treat Williams and Famke Janssen are escaping on the jet ski look closely. You can see it's a male stunt double for Famke due to the nose size.
Chosen answer: According to the DVD commentary, the monsters in the film are a combination of 3 different undersea creatures. All of them are microscopic.
Grumpy Scot