The Hynerpeton is constantly making roar-like sounds. It is highly doubtful the animal was capable of emitting such noises in real life. Or even if it was, roaring non-stop would still be an unrealistic thing for an animal to do.
When the female Cephalaspis jets out of view, escaping from the Brontoscorpio, she starts to disappear before she reaches the edge of the screen. If you freeze-frame here (though the error is visible without freeze-framing), you can see that her upper portion has been "cropped off", and you can clearly see the background through her.
When the scorpions are mauling the Cephalaspis, many of the fish jumping out of the sea aren't reflected in the water. Also in one shot, the reflection of the Brontoscorpio approaching the scene from the background is rendered in such a way, it makes it look like the animal's floating a feet or two above the ground.
When the Brontoscorpio chases after the Cephalaspis, the scorpion's animated as if it walked over a smaller outcropping on its way down the seabed's incline, but there is no such outcropping visible, making it look like the Brontosorpio sank into the incline for a second.
When the Hyneria bumps into a log with its tailfin, the CGI animal is somewhat erroneously inserted into the footage. If you look at its tailfin, a small part of the log it's hitting disappears and reappears around its fin.
After the Pterygotus has killed the Brontoscorpio and starts breaking it to pieces, the pieces drift down behind the Pterygotus, but land in front of it. The animators forgot to put the CGI Pterygotus behind the Brontoscorpio pieces as they fall to the ocean floor.
The goof item below may give away important plot points.
As the Hyneria throws the Hynerpeton back into the water, a strange black shape juts out of the side of its head, then disappears back into it. It appears as though the CGI Hynerpeton's tail clipped though Hyneria's head.
When the Hyneria drags the Hynerpeton into the lake, just before it swims out of frame, the entire tail of the Hynerpeton visibly clips through the fish's forehead. Also in this shot, the waves and splashes on the surface of the water are moving almost in slow-motion with a very low frame-rate, revealing they've been only added digitally onto it.