When the survivors were jumping out of the hole in the end, when Dr. Ballard was jumping out it showed Richard jumping out instead of Dr. Ballard, you can see by the fact that he doesn't have an arm sling.

Also when Dylan jumps out he doesn't have his backpack, with the camera, battery, and tape that he had all during the night, with him. What did he decide to leave it on the ship? (You need to play his jumping out in slow motion to catch this)

Finally the distance of the Seals in their boats from the Poseidon changes from the shot of the ship in a wide shot and the shot from above where the characters can see them from.