When the creature first strikes the ship, we see it attack from under the hull and towards the moving engine propellers. At this point in the film the engines, communication and emergency systems had been disabled by sabotage, hence the propellers should have been idle and not in full motion.
When they board the ship, Finnigan's boat is far below the cargo door; then, when he jumps from the boat in to help Trilian it is at the almost same level - which is plausible since the ship is sinking. However, when they jump on the Ski-Doo to escape, it is again far below the door again.
When Trillian is thrown into the brig, she takes out Canton's wallet that she had pickpocketed. However, all the time they had been talking in the vault, she had been held well away from him, with both hands held behind her back.
At the end of the film, as Finnegan and Trillian arrive on the beach they pull the jet-ski up past the waterline; when Trillian spots Joey, and they run into the waves to help him, the jet-ski is suddenly gone from the beach; as they help Joey out of the water, the surfboard should be right there, where they've lifted him off it, but it's not - it's disappeared as well; and as the unknown creature roars, and the final aerial shot pulls back from the beach, the jet-ski is back again on the beach above the waves, but the surfboard is still missing.
Near the ending when Finnegan is attempting to start the powerboat he turns and holds the key several times before the boat starts. Whenever the camera directly faces the control panel the key is clearly seen without his hand on it.
When Mason says, "I don't mean to sound like a pussy," he is pointing his rifle towards the water where our characters are about to dive in, but then in the next shot when he says, "but this shit is startin' to freak me out, man!" his rifle is pointing in the opposite direction.
Orchestating a sabotage as depicted in the movie is not possible, as modern ships have several on-board computers to prevent, precisely, the case of one of them going offline to cause the whole liner go blind. Furthermore, Maritime law requires every vital of the ship - particularly communications - to have officers on guard at all times, and although Canton owns the ship, he is still a civilian and would not have unlimited access to it.
After the Argonautica is sabotaged, the man at the radar warns about something moving rapidly towards the ship and he is able to tell the speed and distance. Nevertheless, the same man claimed seconds before that they were sailing with "blank screens", and previously the imaging, navigational and communication systems are shown to be "disengaged". How can the officers on the bridge detect the creatures coming if all instruments are down?
When the creatures first strike the boat, and the passengers are running scared, the young Asian woman locks herself in the bathroom. When the creature is sneaking up on her through the toilet that she is sitting on, she frantically grabs the sink faucet. When she first grabs hold of it, you can already see it moving before she pulls it off its hinges.