Factual error: After the ship capsized, the engines (and generators) could not have continued to run inverted due to lubrication and fuel delivery problems. Engines can not run upside down as they will fail due to lack of lubricant, since the pickups are at the bottom. Same for fuel - most fuel pickups are near the bottom of the tank so you can use the full capacity of the tank. With the ship upside down these pickups would fail. Even if battery power could run some emergency lights for a while, there would have been nothing to supply the massive energy needed to run the bow thrusters.
Plot hole: When the ship has turned on its side for the brief moment, it cuts to inside the ship where a hallway explodes, causing the ship to submerge. The only problem is the people are standing on the ceiling, but if the ship's on its side, they'd be on the wall, not ceiling.
Continuity mistake: During the capsizing in the disco, a light rigging falls and knocks some people over. There is a woman in a black top and pink skirt - she falls over twice between the two shots.
Factual error: When performing CPR on Elena, Robert doesn't tilt her head back. As a former firefighter, he would know one of the first steps of CPR is to tilt the victim's head back to clear the airway.
Factual error: Near the end, the characters are fighting against the push or pull of the propellers. This doesn't make sense as both props would be moving air in the same direction at all times, left to right or right to left. Its true there would be an extremely high velocity air jet blowing through the tube, but it would NOT create any significant pressure differential between the inside of the tube and atmosphere (unless they are rotating at different speeds). It would essentially become a wind tunnel with little to no static pressure.
Factual error: In the elevator scene close to the beginning of the movie, the people use quite some force to open the hoist way doors. In reality, they have no motor and can be opened easily, although they often spring shut when released. They would still have to be pried open from the outside, but inside, there's often a knob or lever that unlocks the doors.
Factual error: Toward the end, when they are in the bow thruster room, the ship's seams rupture and water, under high pressure, streams in. They had to drop 30 ft from the bow thruster tube, that room would have been at, or just above the water level. 1) The seams wouldn't have burst like they did, and 2) the water wouldn't have streamed in at such high pressure.
Factual error: In the scene where everyone is in the first ballast tank and the water is turned on, there is air inside the ballast. As the water level rises, the air will become more and more compressed at the top until eventually there should be a thin cushion of air on the top with sufficient pressure to resist any additional flooding. Now I know nothing about the construction of ballast tanks, so there may be a vent on the top to let air out as it fills normally. If there is such a vent, it would now be in the bottom since the ship capsized. So when the characters rise up to the top, that is actually the bottom of the tank with no holes/vents for the air to escape.
Revealing mistake: During the scene in the bow thruster room near the end of the movie, Richard Dreyfuss rushes to the thruster tunnel access hatch to open it. As he grabs hold of the wheel, the hatch and frame visibly move, exposing it as the lightly built set that it is.
Continuity mistake: During the capsize, when the woman falls from above the elevator to her death, she is flipping a different way when she impacts the roof from when she first started falling.
Factual error: After the first ballast tank is flooded, the others are shown filling during the rest of the movie. But since the ship is upside down and the valves therefore at the top of the tank, all of the water is below the valve, and couldn't possibly flow through it to the next tank.