When the tail of the Basilosaurus breaks through the water surface, it is actually clearly the tail of a modern humpback whale.
As the Basilosaurus tears off Nigel's loudspeaker, its edge clips into the CGI animal's lips.
During the end credits, as we see the Megalodon shark swimming under the Ancient Mariner, the light reflections on its body form a repeating pattern that don't correspond with the actual light rays shining through the waves.