The boat used in long shots and the one in close-ups are obviously different.
When McKinley is making his way toward Alec, there is a shot of Edith Middleton looking back at him. In the next shot, she is looking out to sea.
When the boat nearly capsizes, Alec rushes over to help Kelly get back upright. Kelly is curled up nearly underwater in one shot, and the boat is nearly full of water. In the next shot, Kelly is laying a cross the width of the boat, which has very little water in it.
At the beginning of the picture, a grand (or baby grand) piano pops up to the surface, and its strings and harp is intact as one can hear. The interior frame of a piano is usually made of cast iron and needs to be heavy enough to withstand the tons of pressure from all of the taut strings. A piano would not pop to the surface and then float that high, it would sink like a stone.
The movie shows sharks swimming with their dorsal fin out of the water. Sharks do not swim with any fin, or any part of the tail fin, out of the water as doing so is inefficient and would slow the shark down. Sharks do not waste their energy.
It was previously said: "When Holmes climbs aboard the lifeboat, he is wearing only his jockey shorts and his t-shirt (...). In later scenes, his pants are miraculously back on him."
However, when the captain dies Holmes orders his clothes to be taken off his body before he is cast adrift. Holmes is plainly wearing the captain's jacket and cap after that point and, it's reasonable to assume, his trousers.
The rescue ship is flying flag H. Therefore she is entering or leaving harbour, as she is indicating she has a pilot onboard. So the ship can't be in the middle of the ocean.
The amount of floating debris around the lifeboat could have easily been used to keep more people afloat.